Size-controlled macromolecule

ABSTRACT

The present application discloses a substrate that includes a molecular layer of regularly spaced size-controlled macromolecules comprising a polymer comprising branched and linear regions in which a plurality of termini on the branched region are bound to the substrate, and a terminus of the linear region is functionalized.

CROSS-REFERENCE To RELATED APPLICATIONS

The present application claims the benefit of priority to U.S.Provisional Patent Application No. 60/567,844, filed May 3, 2004, and60/571,052, filed May 14, 2004, and PCT/KR03/01913, filed Sep. 18, 2003,PCT/KR03/02261, filed Oct. 24, 2003, and U.S. patent application Ser.No. 10/363,948, filed Sep. 5, 2001, pending.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to the field of hyperbranchedmacromolecules. The present invention relates to the field offunctionalized substrates on which is bound the macromolecules. Thepresent invention also relates to the field of functionalizedsize-controlled dendrimers and dendrons that are used to bind to afunctionalized substrate at one end of the dendron and to atarget-specific ligand on the other end. The present invention alsorelates to the field of combinatorial chemistry, specific proteindetection methods, specific nucleic acid or nucleic acid/peptide hybriddetection methods using a functionalized substrate to which is bound ahyperbranched polymer linked to a probe biomolecule.

2. General Background and State of the Art

Since the first report (Fodor et al., Nature 364, 555-556 (1993); Saikiet al., Proc. Natl. Acad. Sci. USA 86, 6230-6234 (1986)), DNAmicroarrays have attracted a great deal of attention because they allowhigh-throughput analysis of the DNA sequence, genetic variations, andgene expression. It is known that this methodology requires improvementin terms of fidelity, reproducibility, and spot homogeneity that areessential for the standardization and application to human genediagnosis (Hackett et al., Nature Biotechnology 21, 742-743 (2003)).These shortcomings are caused mainly by the variations in the nature ofthe surface and molecular interlayer structures that are far from ideal.Likewise, the field of high-throughput target detection systemsencompasses bioassays utilizing immobilized bioactive molecules andbiomolecules.

Here we show that DNA microarrays fabricated on a nanoscale-controlledsurface discriminates single mismatched pairs as effectively as DNA doesin solution. This approach provides an ideal DNA-microarray in whicheach probe DNA strand is given ample space enough to interact with anincoming target DNA with minimal steric hindrance. The dramaticallyincreased discrimination efficiency promises the very reliable diagnosisof human genes. Moreover, the approach is general enough to be appliedto various bioassays utilizing immobilized bioactive molecules andbiomolecules.

Affinity purification is a well-known technique for the separation andidentification of ligand-binding proteins (Cuatrecasas et al., Proc.Natl. Acad. Sci. U.S.A. 1968, 61, 636-643). A unique interaction betweena ligand covalently attached to an insoluble matrix and thecomplementary target protein provides the specificity required for theisolation of biomolecules from complex mixtures. However, its widespreaduse has been hampered by the limited choice and instability ofconventional matrices. Significant nonspecific binding of proteins tomany solid supports has been a persistent problem in establishing newmatrices (Cuatrecasas, P. J. Biol. Chem. 1970, 245, 3059-3065). It istherefore desirable to find new matrices that are comparable to thetraditional matrices in terms of the specificity while exhibitingenvironmental stability and capability of well-defined and facileattachment of ligands.

Aminopropyl-controlled pore glass (or AMPCPG) that is originally usedfor the solid-phase peptide synthesis appears to have many desirablefeatures. However, the controlled pore glass (or CPG) surface is polarand retains partial negative charge even when coated (Hudson, D. J.Comb. Chem. 1999, 1, 403-457). The feature plays a key role insignificant nonspecific binding of proteins. Therefore, application onboth affinity chromatography and solid-phase peptide synthesis has beenlimited. Once the obstacles are eliminated, widespread use of thematerials can be expected.

Accessibility of ligands is a key factor in determining bindingcapacity. The traditional approaches are introducing a spacer moleculeand increasing the ligand concentration for better exposition of theligand on the surface (Rusin, et al., Biosensors & Bioelectronics 1992,7, 367-373; Suen et al., Ind. Eng. Chem. Res. 2000, 39, 478-487; Penzolet al., Biotechnol and Bioeng. 1998, 60, 518-523; Spinke et al., J.Chem. Phys. 1993, 99, 7012-7019). The approach works to a certaindegree, but insufficient space between the ligands and randomdistribution of capture molecules over the surfaces are the issues yetto be solved (Hearn et al., J. Chromatogr. A. 1990, 512, 23-39; Murza etal., J. Chromatogr. B. 2000, 740, 211-218; Xiao et al., Langmuir 2002,18, 7728-7739). By far two methods have been employed to improve theseshortcomings. One way is to utilize a big molecule such as protein as aplaceholder. The protein is conjugated onto the matrix, and theplaceholder molecule was cleaved off and washed out. In this way,certain distance between the linkers left on the matrix is secured.Nevertheless, choice of the placeholder molecule and design of thedeprotection route have to be elaborately optimized for every differentsituation (Hahn et al., Anal. Chem. 2003, 75, 543-548). Another way isto employ a cone-shape dendron that gives a highly orderedself-assembled monolayer and utilize an active functional group at theapex of the dendron (Xiao et al., Langmuir 2002, 18, 7728-7739;Whitesell et al., Langmuir 2003, 19, 2357-2365).

Here we present modification of AMPCPG with dendrons, further attachmentof GSH at the apex of the dendrons, and characteristics of the surfacematerials in terms of GST proteins binding. A dendron featuring three ornine carboxylic acid groups at the termini and one amine group at theapex has been introduced into the matrices. Their carboxylic groups werecovalently linked with the solid surface. Due to wide use andunderstating of glutathione S-transferase (or GST) gene fusion system,glutathione was chosen as a ligand to be tethered on the dendron-treatedmatrix. Ligand binding property of the matrix has been investigated withGST and two fusion proteins (GST-PX^(P47), GST-Munc-18) (Smith et al.,Gene 1988, 67, 31-40; Sebastian et al., Chromatogr. B. 2003, 786,343-355; Wu et al., Chromatogr. B. 2003, 786, 177-185; De Carlos et al.,J. Chromatogr. B. 2003, 786, 7-15).

SUMMARY OF THE INVENTION

The present invention provides a substrate bound thereonsize-controlled, preferably cone shaped molecules linked to a ligand.

The present invention is directed to a substrate comprising a molecularlayer of regularly spaced size-controlled macromolecules comprising apolymer comprising branched and linear regions in which a plurality oftermini on the branched region are bound to the substrate, and aterminus of the linear region is functionalized. On the substrate, themacromolecules may be spaced at regular intervals. In particular, themacromolecules may be spaced at regular intervals between about 0.1 nmand about 100 nm between the linear functionalized groups. Inparticular, the macromolecules may be spaced at regular intervals ofabout 10 nm.

In the above-described substrate, the terminus of the branched regionmay be functionalized with —COZ, —NHR, —OR′, or —PR″₃, wherein Z may bea leaving group, wherein R may be an alkyl, wherein R′ may be alkyl,aryl, or ether, and R″ may be H, alkyl, alkoxy, or O. In particular, COZmay be ester, activated ester, acid halide, activated amide, orCO-imiazoyl; R may be C₁-C₄ alkyl, and R′ may be C₁-C₄ alkyl. Further,in the above described substrate, the polymer may be a dendron. Stillfurther, the linear region of the polymer may be comprised of a spacerregion. And the spacer region may be connected to the branched regionvia a first functional group. Such first functional group may be withoutlimitation —NH₂, —OH, —PH₃, —COOH, —CHO, or —SH. Still further, thespacer region may comprise a linker region covalently bound to the firstfunctional group.

In the substrate described above, the linker region may comprise asubstituted or unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl, aryl,ether, polyether, ester, or aminoalkyl group. Still further, spacerregion may comprise a second functional group. The second functionalgroup may include without limitation —NH₂, —OH, —PH₃, —COOH, —CHO, or—SH. The second functional group may be located at the terminus of thelinear region. And a protecting group may be bound to the terminus ofthe linear region. Such protecting group may be acid labile or baselabile.

In another embodiment of the invention, in the substrate as describedabove, a target-specific ligand may be bound to the terminus of thelinear region. In particular, the target-specific ligand may be achemical compound, DNA, RNA, PNA, aptamer, peptide, polypeptide,carbohydrate, antibody, antigen, biomimetics, nucleotide analog, or acombination thereof. Further, the distance between the target-specificligands bound to the linear region of the macromolecules may be fromabout 0.1 to about 100 nm.

In yet another embodiment of the invention, the substrate describedabove may be made of semiconductor, synthetic organic metal, syntheticsemiconductor, metal, alloy, plastic, silicon, silicate, glass, orceramic. In particular, the substrate may be without limitation a slide,particle, bead, micro-well, or porous material. The porous material maybe a membrane, gelatin or hydrogel. And further in particular, the beadmay be a controlled pore bead.

The invention is also directed to a method for manufacturing a molecularlayer of regularly spaced size-controlled macromolecules comprising apolymer comprising branched and linear regions in which a plurality oftermini on the branched region are bound to the substrate, and aterminus of the linear region is functionalized, comprising:

-   -   (i) functionalizing the substrate so that it will react with the        termini of the macromolecules; and    -   (ii) contacting the macromolecules to the substrate so that the        termini and the substrate form a bond.

In this method, the substrate may be made of without limitationsemiconductor, synthetic organic metal, synthetic semiconductor, metal,alloy, plastic, membrane, silicon, silicate, glass, or ceramic. Thesubstrate may be a slide, bead, microwell, or porous material. Theporous material may be a hydrogel, gelatin, or membrane. The bead may bea controlled pore bead.

Further, in the method described above, a target-specific ligand isfixed to the terminus of the linear region, comprising the steps of

-   -   i) removing protecting group from the terminus of the linear        region of the macromolecules on the substrate; and    -   ii) contacting the target-specific ligand or a linker molecule        linked to the target-specific ligand to the terminus of the        linear region of the macromolecules on the substrate so that the        ligand or the linker molecule and the terminus form a bond,        wherein the linker molecule is a homobifunctional or        heterobifunctional linker.

In this method, the presence of the macromolecules on the substrateresults in minimal interference in the binding of the target-specificligand to the linear termini. Further in this method, the presence ofthe macromolecules on the substrate results in minimal interference inthe detection of a target specific to the target-specific ligand. Stillfurther, the target-specific ligand may be spaced at regular intervals.In particular, the target-specific ligands may be placed on thesubstrate at a low density. In the above-described method, thetarget-specific ligand may be a chemical compound, DNA, RNA, PNA,aptamer, peptide, polypeptide, enzyme, carbohydrate, polysaccharide,antibody, antigen, biomimetics, nucleotide analog, or a combinationthereof.

In another embodiment, the invention is also directed to a diagnosticsystem for detecting a mutation in a gene, comprising theabove-described substrate, wherein the terminus of the linear region isfixed with target specific oligonucleotides. Such oligonucleotides maybe specific for cancer related genes. In particular, the cancer relatedgene may be p53.

In still another embodiment, the invention is directed to a method fordetecting presence of a mutation in a gene, comprising contacting theabove-described substrate with a sample containing the gene to beassayed, wherein the terminus of the linear region is fixed with atarget specific oligonucleotide. In this method, the gene may be acancer related gene. Further, the gene may be p53.

These and other objects of the invention will be more fully understoodfrom the following description of the invention, the referenced drawingsattached hereto and the claims appended hereto.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention will become more fully understood from thedetailed description given wherein below, and the accompanying drawingswhich are given by way of illustration only, and thus are not limitativeof the present invention, and wherein;

FIG. 1 shows Formula I, which is a branched/linear polymer or asize-controlled macromolecule.

FIG. 2 shows a reaction scheme for producing a dendron. X represents aprotecting group.

FIGS. 3 a-3 c show detection of a dendron-modified surface. FIG. 3 ashows a scheme for surface modification and hybridization. FIG. 3 bshows the molecular structure of the employed dendron. FIG. 3 c showsthe DNA sequence of the probe and target DNA strands. Probeoligonucleotides include Probe 1: 5′-NH₂-C₆-CAT TCC GNG TGT CCA-3′ (SEQID NO:1) and Probe 2: 5′-NH₂-C₆-(T)₃₀-CAT TCC GNG TGT CCA-3′ (SEQ IDNO:2). Target nucleotides include Target 1: 5′-Cy3-TGG ACA CTC GGAATG-3′ (SEQ ID NO:3) and Target 2: 5′-Cy3-CCT ACG AAA TCT ACT GGA ACGAAA TCT ACT TGG ACA CTC GGA ATG-3′ (SEQ ID NO:4).

FIGS. 4 a-4 b show UV spectroscopic analysis. (a) shows UV spectrumafter each reaction step. EG/GPDS and Dendron signify spectra acquiredbefore and after the introduction of the dendron on the ethyleneglycol-modified substrate, and Deblock corresponds to the spectrum afterthe deprotection step. (b) shows stability test. A spectrum obtainedafter stirring in DMF at room temperature for 1 d is signified by“Washing”.

FIG. 5 shows tapping mode atomic force microscopy (AFM) image of thedendron-modified surface. A Nanoscope IIIa AFM (Digital Instruments)equipped with an “E” type scanner was employed. The scanned area is1.0×1.0 μm².

FIGS. 6 a-6 d show fluorescence images after hybridization. 6a-6b showimages obtained after the hybridization between (a) probe 1 and target 1or (b) probe 1 and target 2 on the dendron-modified surface. 6c-6d showimages recorded after the hybridization between (c) target 1 and probe 1or (d) target 1 and probe 2 on an APDES-modified surface.

FIGS. 7 a-7 f show differences in intensity between matched and theinternally mismatched pairs of oligonucleotides. Upper images (a-c) are4×4 array fluorescence images and lower images (d-f) show one spotsampled from the 16 spots. (a) and (d) are for a dendron-modifiedmicroarray with DSC linker, (b) and (e) for an APDES-modified microarraywith PDITC linker, and (c) and (f) for an APDES-modified microarray withDSC linker. Fluorescence images for a dendron-modified microarray withDSC linker and a APDES-modified microarray with PDITC linker show lessthan 10% coefficient variance (CV) value and homogeneous fluorescencesignal in a single spot. On the other side, fluorescence images for anAPDES-modified microarray with DSC linker show much smaller spot size,over 20% CV value, and non-uniform fluorescence signal in a single spot.Each pixel size is 10×10 μm².

FIGS. 8 a-8 b show fluorescence images after hybridization of p53specific oligonucleotide probe to target DNA sample for detection ofsingle mutation in p53 using (a) [9]-acid dendron; and (b) [27]-aciddendron.

FIGS. 9 a-9 b show simultaneous detection of 7 hotspots of p53 Gene.

FIG. 10 shows a schematic presentation of sample E1 (Fmoc-(3)acid) andE3 (Fmoc-(9)acid) preparation with the dendrons on AMPCPG matrices,deprotection of Fmoc group by 20% piperidine in DMF and theincorporation of glutathione.

FIG. 11 shows binding of purified GST and GST lysate using three typesof beads. M: markers. For comparison, GST lysate is run directly (lane1). As controls, binding of the purified GST was tested for the matrices(A, E1, and E3) (lane 2, 3, 4). Finally, binding of cell lysate wasexamined to investigate efficiency of the matrices (A, E1, and E3) (lane5, 6, 7).

FIG. 12 shows a protected first generation functionalized dendron (E1,Fmoc-(3)acid), and a protected second generation functionalized dendron(E3, Fmoc-(9)acid).

FIG. 13 shows binding of GST from cell lysate was recorded for twocontrol beads, CL and CS in comparison with E1 and E3. M: markers; Lane1: CL; Lane 2: CS; Lane 3: E1; Lane 4: E3.

FIG. 14 shows three fused GST proteins (GST (28 kDa), GST-PX^(p47) (41kDa), and GST-Mucnc 18 (98 kDa)) were employed to examine change of thebinding capacity. Relative binding capacity of three matrices wasmeasured with a densitiometer. Binding capacity of all matrices is setto be 100% for GST. Sepharose-4B (filled circle); E1 (filled square); E3(open triangle).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

In the present application, “a” and “an” are used to refer to bothsingle and a plurality of objects.

As used herein, “aptamer” means a single-stranded, partiallysingle-stranded, partially double-stranded or double-stranded nucleotidesequence, advantageously replicatable nucleotide sequence, capable ofspecifically recognizing a selected nonoligonucleotide molecule or groupof molecules by a mechanism other than Watson-Crick base pairing ortriplex formation.

As used herein, “bifunctional,” “trifunctional” and “multifunctional,”when used in reference to a synthetic polymer or multivalent homo- orheteropolymeric hybrid structure, mean bivalent, trivalent ormultivalent, as the case may be, or comprising two, three or multiplespecific recognition elements, defined sequence segments or attachmentsites.

As used herein, “biomimetic” means a molecule, group, multimolecularstructure or method that mimics a biological molecule, group ofmolecules, structure.

As used herein, “dendritic molecule” is a molecule exhibiting regulardendritic branching, formed by the sequential or generational additionof branched layers to or from a core.

As used herein, “dendritic polymer” is a polymer exhibiting regulardendritic branching, formed by the sequential or generational additionof branched layers to or from a core. The term dendritic polymerencompasses “dendrimers”, which are characterized by a core, at leastone interior branched layer, and a surface branched layer (see, e.g.,Petar et al. Pages 641-645 In Chem. in Britain, (August 1994). A“dendron” is a species of dendrimer having branches emanating from afocal point, which is or can be joined to a core, either directly orthrough a linking moiety to form a dendrimer. Many dendrimers comprisetwo or more dendrons joined to a common core. However, the termdendrimer may be used broadly to encompass a single dendron.

Dendritic polymers include, but are not limited to, symmetrical andasymmetrical branching dendrimers, cascade molecules, arborols, and thelike. In a preferred embodiment, the branch arms may be of equal length.The branching may typically occur without limitation at the hydrogenatoms of a terminal —NH₂ group on a preceding generation branch, forexample. However, it is also contemplated that asymmetric dendimers mayalso be used. For instance, lysine-based dendrimers are asymmetric, inthat the branch arms are of a different length. One branch occurs at theepsilon nitrogen of the lysine molecule, while another branch occurs atthe alpha nitrogen, adjacent to the reactive carboxy group whichattaches the branch to a previous generation branch.

Further, it is understood that even though not formed by regularsequential addition of branched layers, hyperbranched polymers, e.g.,hyperbranched polyols, may be equivalent to a dendritic polymer wherethe branching pattern exhibits a degree of regularity approaching thatof a dendrimer.

As used herein, “hyperbranched” or “branched” as it is used to describea macromolecule or a dendron structure is meant to refer to a pluralityof polymers having a plurality of termini which are able to bindcovalently or ionically to a substrate. In one embodiment, themacromolecule comprising the branched or hyperbranched structure is“pre-made” and is then attached to a substrate. Accordingly, theinventive macromolecule excludes polymer cross-linking methods asdisclosed in U.S. Pat. No. 5,624,711 (Sundberg et al.).

As used herein, “immobilized” means insolubilized or comprising,attached to or operatively associated with an insoluble, partiallyinsoluble, colloidal, particulate, dispersed, suspended and/ordehydrated substance or a molecule or solid phase comprising or attachedto a solid support.

As used herein, “library” refers to a random or nonrandom mixture,collection or assortment of molecules, materials, surfaces, structuralshapes, surface features or, optionally and without limitation, variouschemical entities, monomers, polymers, structures, precursors, products,modifications, derivatives, substances, conformations, shapes, orfeatures.

As used herein, “ligand” means a selected molecule capable ofspecifically binding to another molecule by affinity-based attraction,which includes complementary base pairing. Ligands include, but are notlimited to, nucleic acids, various synthetic chemicals, receptoragonists, partial agonists, mixed agonists, antagonists,response-inducing or stimulus molecules, drugs, hormones, pheromones,transmitters, autacoids, growth factors, cytokines, prosthetic groups,coenzymes, cofactors, substrates, precursors, vitamins, toxins,regulatory factors, antigens, haptens, carbohydrates, molecular mimics,structural molecules, effector molecules, selectable molecules, biotin,digoxigenin, crossreactants, analogs, competitors or derivatives ofthese molecules as well as library-selected nonoligonucleotide moleculescapable of specifically binding to selected targets and conjugatesformed by attaching any of these molecules to a second molecule.

As used herein, “linker molecule,” and “linker” when used in referenceto a molecule that joins the branched portion of a size-controlledmacromolecule such as a branched/linear polymer to a protecting group ora ligand. Linkers may include, for instance and without limitation,spacer molecules, for instance selected molecules capable of attaching aligand to a dendron.

As used herein, “low density” refers to about 0.01 to about 0.5probe/nm², preferably about 0.05 to about 0.2, more preferably about0.075 to about 0.15, and most preferably about 0.1 probe/nm².

As used herein, “molecular mimics” and “mimetics” are natural orsynthetic nucleotide or nonnucleotide molecules or groups of moleculesdesigned, selected, manufactured, modified or engineered to have astructure or function equivalent or similar to the structure or functionof another molecule or group of molecules, e.g., a naturally occurring,biological or selectable molecule. Molecular mimics include moleculesand multimolecular structures capable of functioning as replacements,alternatives, upgrades, improvements, structural analogs or functionalanalogs to natural, synthetic, selectable or biological molecules.

As used herein, “nucleotide analog” refers to molecules that can be usedin place of naturally occurring bases in nucleic acid synthesis andprocessing, preferably enzymatic as well as chemical synthesis andprocessing, particularly modified nucleotides capable of base pairingand optionally synthetic bases that do not comprise adenine, guanine,cytosine, thymidine, uracil or minor bases. This term includes, but isnot limited to, modified purines and pyrimidines, minor bases,convertible nucleosides, structural analogs of purines and pyrimidines,labeled, derivatized and modified nucleosides and nucleotides,conjugated nucleosides and nucleotides, sequence modifiers, terminusmodifiers, spacer modifiers, and nucleotides with backbonemodifications, including, but not limited to, ribose-modifiednucleotides, phosphoramidates, phosphorothioates, phosphonamidites,methyl phosphonates, methyl phosphoramidites, methyl phosphonamidites,5′-β-cyanoethyl phosphoramidites, methylenephosphonates,phosphorodithioates, peptide nucleic acids, achiral and neutralinternucleotidic linkages and normucleotide bridges such as polyethyleneglycol, aromatic polyamides and lipids.

As used herein, “polymer” or “branched/linear polymer” refers to amolecule having a branched structure at one end of the molecule and alinear portion at the other end so that the branched portion binds to asubstrate and the linear portion binds to a ligand, probe or aprotecting group.

As used herein, “polypeptide”, “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidue is an artificial chemical analogue of a corresponding naturallyoccurring amino acid, as well as to naturally occurring amino acidpolymers. The term may also include variants on the traditional peptidelinkage joining the amino acids making up the polypeptide.

As used herein, “protecting group” refers to a group that is joined to areactive group (e.g., a hydroxyl or an amine) on a molecule. Theprotecting group is chosen to prevent reaction of the particular radicalduring one or more steps of a chemical reaction. Generally theparticular protecting group is chosen so as to permit removal at a latertime to restore the reactive group without altering other reactivegroups present in the molecule. The choice of a protecting group is afunction of the particular radical to be protected and the compounds towhich it will be exposed. The selection of protecting groups is wellknown to those of skill in the art. See, for example Greene et al.,Protective Groups in Organic Synthesis, 2nd ed., John Wiley & Sons, Inc.Somerset, N.J. (1991), which is incorporated by reference herein in itsentirety.

As used herein, “protected amine” refers to an amine that has beenreacted with an amino protecting group. An amino protecting groupprevents reaction of the amide function during attachment of thebranched termini to a solid support in the situation where the lineartip functional group is an amino group. The amino protecting group canbe removed at a later time to restore the amino group without alteringother reactive groups present in the molecule. For example, theexocyclic amine may be reacted with dimethylformamide diethylacetal toform the dimethylaminomethylenamino function. Amino protecting groupsgenerally include carbamates, benzyl radicals, imidates, and othersknown to those of skill in the art. Preferred amino protecting groupsinclude, but are not limited to, p-nitrophenylethoxycarbonyl ordimethyaminomethylenamino.

As used herein, “regular intervals” refers to the spacing between thetips of the size-controlled macromolecules, which is a distance fromabout 1 nm to about 100 nm so as to allow room for interaction betweenthe target-specific ligand and the target substantially without sterichindrance. Thus, the layer of macromolecules on a substrate is not toodense so that specific molecular interactions may occur.

As used herein, “solid support” refers to a composition comprising animmobilization matrix such as but not limited to, insolubilizedsubstance, solid phase, surface, substrate, layer, coating, woven ornonwoven fiber, matrix, crystal, membrane, insoluble polymer, plastic,glass, biological or biocompatible or bioerodible or biodegradablepolymer or matrix, microparticle or nanoparticle. Solid supportsinclude, for example and without limitation, monolayers, bilayers,commercial membranes, resins, matrices, fibers, separation media,chromatography supports, polymers, plastics, glass, mica, gold, beads,microspheres, nanospheres, silicon, gallium arsenide, organic andinorganic metals, semiconductors, insulators, microstructures andnanostructures. Microstructures and nanostructures may include, withoutlimitation, microminiaturized, nanometer-scale and supramolecularprobes, tips, bars, pegs, plugs, rods, sleeves, wires, filaments, andtubes.

As used herein, “spacer molecule” refers to one or more nucleotideand/or normucleotide molecules, groups or spacer arms selected ordesigned to join two nucleotide or normucleotide molecules andpreferably to alter or adjust the distance between the two nucleotide ornormucleotide molecules.

As used herein, “specific binding” refers to a measurable andreproducible degree of attraction between a ligand and its specificbinding partner or between a defined sequence segment and a selectedmolecule or selected nucleic acid sequence. The degree of attractionneed not be maximized to be optimal. Weak, moderate or strongattractions may be appropriate for different applications. The specificbinding which occurs in these interactions is well known to thoseskilled in the art. When used in reference to synthetic defined sequencesegments, synthetic aptamers, synthetic heteropolymers, nucleotideligands, nucleotide receptors, shape recognition elements, andspecifically attractive surfaces. The term “specific binding” mayinclude specific recognition of structural shapes and surface features.Otherwise, specific binding refers explicitly to the specific,saturable, noncovalent interaction between two molecules (i.e., specificbinding partners) that can be competitively inhibited by a thirdmolecule (i.e., competitor) sharing a chemical identity (i.e., one ormore identical chemical groups) or molecular recognition property (i.e.,molecular binding specificity) with either specific binding partner. Thecompetitor may be, e.g., a crossreactant, or analog of an antibody orits antigen, a ligand or its receptor, or an aptamer or its target.Specific binding between an antibody and its antigen, for example, canbe competitively inhibited either by a crossreacting antibody or by acrossreacting antigen. The term “specific binding” may be used forconvenience to approximate or abbreviate a subset of specificrecognition that includes both specific binding and structural shaperecognition.

As used herein, “substrate,” when used in reference to a substance,structure, surface or material, means a composition comprising anonbiological, synthetic, nonliving, planar, spherical or flat surfacethat is not heretofore known to comprise a specific binding,hybridization or catalytic recognition site or a plurality of differentrecognition sites or a number of different recognition sites whichexceeds the number of different molecular species comprising thesurface, structure or material. The substrate may include, for exampleand without limitation, semiconductors, synthetic (organic) metals,synthetic semiconductors, insulators and dopants; metals, alloys,elements, compounds and minerals; synthetic, cleaved, etched,lithographed, printed, machined and microfabricated slides, devices,structures and surfaces; industrial polymers, plastics, membranes;silicon, silicates, glass, metals and ceramics; wood, paper, cardboard,cotton, wool, cloth, woven and nonwoven fibers, materials and fabrics;nanostructures and microstructures unmodified by immobilization probemolecules through a branched/linear polymer.

As used herein, “target-probe binding” means two or more molecules, atleast one being a selected molecule, attached to one another in aspecific manner. Typically, a first selected molecule may bind to asecond molecule that either indirectly, e.g., through an interveningspacer arm, group, molecule, bridge, carrier, or specific recognitionpartner, or directly, i.e., without an intervening spacer arm, group,molecule, bridge, carrier or specific recognition partner,advantageously by direct binding. A selected molecule may specificallybind to a nucleotide via hybridization. Other noncovalent means forconjugation of nucleotide and normucleotide molecules include, e.g.,ionic bonding, hydrophobic interactions, ligand-nucleotide binding,chelating agent/metal ion pairs or specific binding pairs such asavidin/biotin, streptavidin/biotin, anti-fluorescein/fluorescein,anti-2,4-dinitrophenol (DNP)/DNP, anti-peroxidase/peroxidase,anti-digoxigenin/digoxigenin or, more generally, receptor/ligand. Forexample, a reporter molecule such as alkaline phosphatase, horseradishperoxidase, β-galactosidase, urease, luciferase, rhodamine, fluorescein,phycoerythrin, luminol, isoluminol, an acridinium ester or a fluorescentmicrosphere which is attached, e.g., for labeling purposes, to aselected molecule or selected nucleic acid sequence using avidin/biotin,streptavidin/biotin, anti-fluorescein/fluorescein,anti-peroxidase/peroxidase, anti-DNP/DNP, anti-digoxigenin/digoxigeninor receptor/ligand (i.e., rather than being directly and covalentlyattached) may be conjugated to the selected molecule or selected nucleicacid sequence by means of a specific binding pair.

Macromolecule Polymer Formulation

FIG. 1 diagram may be referred to in describing the inventive polymer.Various R, T. W, L, and X group variables are noted in FIG. 1. Theinventive macromolecule polymer may comprise any branched orhyperbranched, symmetrical or asymmetrical polymer. The branched terminiof the polymer may bind to the substrate preferably by a plurality ofthe termini. The linear end of the polymer may end with a functionalgroup to which may be attached a protecting group or a target-specificligand. The distance between the probes among the plurality of polymerson a substrate may be from about 0.1 nm to about 100 nm, preferablyabout 1 nm to about 100 nm, preferably, about 2 nm to about 70 nm, morepreferably about 2 nm to about 60 nm, most preferably about 2 nm toabout 50 nm.

R-Group

Referring to Formula I set forth in FIG. 1, the polymer generallycomprises a branched section, wherein a plurality of the ends arefunctionalized to bind to a substrate. Within this branched section, thefirst generation group of branches R_(x) (R₁, R₂, R₃) is connected to asecond generation group of branches R_(xx) (R₁₁, R₁₂, R₁₃, R₂₁, R₂₂,R₂₃, R₃₁, R₃₂, R₃₃) by a functional group, W. The second generationgroup of branches is connected to a third generation group of branchesR_(xxx) (R₁₁₁, R₁₁₂, R₁₁₃, R₁₂₁, R₁₂₂, R₁₂₃, R₁₃₁, R₁₃₂, R₁₃₃, R₂₁₁,R₂₁₂, R₂₁₃, R₂₂₁, R₂₂₂, R₂₂₃, R₂₃₁, R₂₃₂, R₂₃₃, R₃₁₁, R₃₁₂, R₃₁₃, R₃₂₁,R₃₂₂, R₃₂₃, R₃₃₁, R₃₃₂, R₃₃₃) by a functional group W. And furtherfourth generation may be connected to the third generation branches inlike fashion. The terminal R group is functionalized so that it iscapable of binding to the substrate.

The R groups of all generations may be the same or different. Typically,the R group may be a repeating unit, a linear or branched organicmoiety, such as but not limited to alkyl, alkenyl, alkynyl, cycloalkyl,aryl, ether, polyether, ester, aminoalkyl, and so on. However, it isalso understood that not all of the R groups need to be the samerepeating unit. Nor do all valence positions for the R group need befilled with a repeating unit. For instance, in the first generationbranch, R_(x), R₁, R₂, R₃ all of the R groups at this branch level maybe the same repeating units. Or, R₁ may be a repeating unit, and R₂ andR₃ may be H or any other chemical entity. Or, R₂ may be a repeatingunit, and R₁ and R₃ may be H or any other chemical entity. Likewise, forthe second and third generation branches, any R group may be a repeatingunit, H or any other chemical entity.

Thus, a variety of shapes of polymers may be made in this way, forinstance, if R₁, R₁, R₁₁₁, R₁₁₂ and R₁₁₃ are the same repeating units,and all other R groups are H's or any number of small neutral moleculeor atom, then a fairly long and thin polymer having a branch with threefunctional group termini for R₁₁₁, R₁₁₂ and R₁₁₃ is made. A variety ofother optional chemical configurations are possible. Thus, it ispossible to obtain from about 3 to about 81 termini having a functionalgroup capable of binding to a substrate. A preferable number of terminimay be from about 3 to about 75, from about 3 to about 70, from about 3to about 65, from about 3 to about 60, from about 3 to about 55, fromabout 3 to about 50, from about 3 to about 45, from about 3 to about 40,from about 3 to about 35, from about 3 to about 30, from about 3 toabout 27, from about 3 to about 25, from about 3 to about 21, from about3 to about 18, from about 3 to about 15, from about 3 to about 12, fromabout 3 to about 9, or from about 3 to about 6.

T-Terminal Group

Terminal groups, T, are functional groups that are sufficiently reactiveto undergo addition or substitution reactions. Examples of suchfunctional groups include without limitation amino, hydroxyl, mercapto,carboxyl, alkenyl, allyl, vinyl, amido, halo, urea, oxiranyl,aziridinyl, oxazolinyl, imidazolinyl, sulfonato, phosphonato,isocyanato, isothiocyanato, silanyl, and halogenyl.

W-Functional Group

In Formula I in FIG. 1, W may be any functional group that may link apolymer to another (or any other divalent organic moiety), such as butnot limited to ether, ester, amide, ketone, urea, urethane, imide,carbonate, carboxylic acid anhydride, carbodiimide, imine, azo group,amidine, thiocarbonyl, organic sulphide, disulfide, polysulfide, organicsulphoxide, sulphite, organic sulphone, sulphonamide, sulphonate,organic sulphate, amine, organic phosphorous group, alkylene,alkyleneoxide, alkyleneamine and so on.

L—Spacer or Linker Group

In FIG. 1, the linear portion of the polymer may include a spacer domaincomprised of a linker region optionally interspersed with functionalgroups. The linker region may be comprised of a variety of polymers. Thelength of the linker may be determined by a variety of factors,including the number of branched functional groups binding to thesubstrate, strength of the binding to the substrate, the type of R groupthat is used, in particular, the type of repeating unit that is used,the type of the protecting group or target specific ligand that is to beattached at the apex of the linear portion of the polymer. Therefore, itis understood that the linker is not to be limited to any particulartype of polymer or of any particular length. However, as a generalguideline, the length of the linker may be from about 0.5 nm to about 20nm, preferably, about 0.5 nm to about 10 nm, and most preferably about0.5 nm to about 5 nm.

The chemical construct of the linker may include without limitation, alinear or branched organic moiety, such as but not limited tosubstituted or unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, aryl, ether, polyether, ester, aminoalkyl,polyalkenylglcol and so on. The linker may further include functionalgroups such as those described above, and as such is not limited to anyparticular structure.

The linker group functionalized at the tip may comprise a protectivegroup. Thus, in one aspect, the present invention is directed to asubstrate to which is attached a plurality of branched/linear polymerscomprising linear tip attached to a protective group. Such a substratemay be chemically reacted to strip off the protective group to bereplaced with a target specific ligand. Therefore, in a functional useof the present inventive system, a substrate bound with a population ofbranched/linear polymers linked to a library of target specific ligandsis provided.

X—Protecting Group

The choice of protecting group depends on numerous factors such as thedesirability of acid-labile or base-lability. Therefore, the inventionis not limited to any particular protecting group so long as it servesthe function of preventing the reaction of the functional group toanother chemical entity, and that it is capable of being stripped underdesired specified conditions. Preferably, the protecting group is easilystripped away. Examples of such protecting groups that may be used inthe present invention include without limitation the following:

Amino acid protecting groups: Methyl, Formyl, Ethyl, Acetyl, t-Butyl,Anisyl, Benzyl, Trifluroacetyl, N-hydroxysuccinimide,t-Butyloxycarbonyl, Benzoyl, 4-Methylbenzyl, Thioanizyl, Thiocresyl,Benzyloxymethyl, 4-Nitrophenyl, Benzyloxycarbonyl,2-Nitrobenzoyl,2-Nitrophenylsulphenyl, 4-Toluenesulphonyl, Pentafluorophenyl,Diphenylmethyl (Dpm), 2-Chlorobenzyloxycarbonyl, 2,4,5-trichlorophenyl,2-bromobenzyloxycarbonyl, 9-Fluorenylmethyloxycarbonyl, Triphenylmethyl,2,2,5,7,8-pentamethyl-chroman-6-sulphonyl, Phthaloyl, 3-Nitrophthaloyl,4,5-dichlorophthaloyl, tetrabromophthaloyl, tetrachlorophthaloyl.

Protecting groups for alcohols: p-Anisyloxymethyl (p-AOM),Benzyloxymethyl (BOM), t-Butoxymethyl, 2-Chlorotetrahydrofuran (THF),Guaiacolmethyl (GUM), (1R)-Menthoxymethyl (MM), p-Methoxybenzyloxymethyl(PMBM), metoxyethoxymethyl (MEM), Methoxymethyl (MOM),o-Nitrobenzyloxymethyl, (Phenyldimethylsilyl)methoxymethyl (SMOM),

2-(Trimethylsilyl)ethoxymethyl (SEM).

DNA, RNA protecting reagent: 2′-OMe-Ac-C-CE Phosphoramidite,2′-OMe-Ac-RNA CPG, 2′-OMe-1-CE Phosphoramidite, 2′-OMe-5-Me-C-CEPhosphoramidite, Ac-C-CE Phosphoramidite, Ac-C-RNA 500, dmf-dG-CEPhosphoramidite, dmf-dG-CPG 500, 2-Amino-dA-CE Phosphoramidite, (M. P.Reddy, N. B. Hanna, and F. Farooqui, Tetrahedron Lett., 1994, 35,4311-4314; B. P. Monia, et al., J. Biol. Chem., 1993, 268, 14514-14522).

Common Protecting Reagents in Organic Syntheses:(Dimethyl-t-butylsilyloxy)methyl chloride (SOMCI), Ethoxyethyl chloride(EECI), α-chloro ethers, o-Nitrobenzyloxymethyl chloride,b,b,b-Trichloroethoxymethyl chloride (TCEMCI), (−)-Menthyl ester,(P)-Benzyl ester, 1,1,1,3,3,3-Hexafluoro-2-phenyl-2-propyl ether,1,1,3,3-Tetramethyl-1,3,2-disilazane, 1,2,4-Dithiazolidine-3,5-dione,1,2-Dibromide, 1,2-Dichloride, 1,2-Diol mono-4-methoxybenzyl ether,1,2-Diol mono-t-butyl ether, 1,2-Diol monoacetate ester, 1,2-Diolmonoallyl ether, 1,2-Diol monobenzoate ester, 1,2-Diol monobenzyl ether,1,2-Diol monotosylate, 1,3-Benzodithiolan, 1,3-Benzodithiolan-2-ylether, 1,3-Diol mono-4-methoxybenzyl ether, 1,3-Diol monobenzoate ester,1,3-Diol monobenzyl ether, 1,3-Dioxan,1-(2-(Trimethoxysilyl)ethoxy)ethyl ether, 1-Adamantyl ester,1-Benzoyl-1-propen-2-yl amine, 1-Ethoxyethyl ether, 1-Methoxyethylideneacetal, 1-Methyl-1-methoxyethyl ether,1-Phenyl-3,5-di-t-butylcyclohexadien-4-onyl amine, 1-Phenylethyl ester,2,2,2-Trichloroethoxymethyl ether, 2,2,2-Trichloroethyl carbonate,2,2,2-Trichloroethyl ester, 2,2,2-Trichloroethyl phosphate,2,2,5,7,8-Pentamethylchroman-6-sulphonamide, 2,2-Dimethyl-4-pentenoateester, 2,3,6-Trimethyl-4-methoxybenzenesulphonamide,2,4,6-Trimethylbenzenesulphonamide, 2,4-DNP hydrazone,2,5-Dichlorophenyl phosphate, 2,5-Dimethylpyrrole,2-(2-Methoxyethoxy)ethyl ester, 2-(4-Nitrophenyl)ethyl ether,2-(4-Nitrophenyl)ethyl phosphate, 2-(4-Toluenesulphonyl)ethyl ester,2-(Dibromomethyl)benzoate ester, 2-(Trimethylsilyl)ethyl carbonate,2-(Trimethylsilyl)ethyl ester, 2-(Trimethylsilyl)ethyl ether,2-Benzenesulphonylethyl thioether, 2-Bromoethyl ester, 2-Chloroethylester, 2-Chlorophenyl phosphate, 2-Cyanoethyl phosphate, 2-Methoxyethylester, 2-Nitrobenzenesulphenamide, 2-Nitrobenzenesulphonamide,2-Oxazoline, 2-Phenylethyl ester, 2-Pyridyl disulphide,2-Tetrahydropyranyl amine, 4-Chlorobenzoate ester, 4-Chlorobutyl ester,4-Methoxybenzamide, 4-Methoxybenzoate ester, 4-Methoxybenzyl amine,4-Methoxybenzyl ester, 4-Methoxybenzyloxymethyl ether, 4-Nitrobenzamide,4-Nitrobenzoate ester, 4-Nitrobenzyl ester, 4-Nitrobenzyl ether,4-Nitrobenzyl phosphate, 4-Nitrophenyl ester, 4-Nitrophenyl hydrazone,4-Toluenesulphonamide, 4-Toluenesulphonate, 9-Fluorenylmethyl carbonate,9-Fluorenylmethyl ester, Allyl carbonate, Allyl ester,Benzenesulphonamide, Benzenesulphonate, Benzyl carbonate, Benzyl ester,BOM ether, DMTr ether, MEM ether, Methanesulphonamide,Methanesulphonate, ethyl carbonate, MMTr ether, MOM carbonate, MOMester, MOM ether, MTHP ether, MTM ester, MTM ether, N-4-Methoxybenzylamide, N-4-Tolyl amide, N-Benzenesulphonyl amide, N-Benzyl imine,n-Butyl ester, n-Butyl ether, O-4-Methoxybenzyl carbamate,0-9-Fluorenylmethyl carbamate, Phenyl thioether, PhenylthiolesterPiperidinamide, PMB ether, SEM ester, SEM ether, Succinateester, t-Butyl carbonate, t-Butyl ester, t-Butyl ether, t-Butylphosphate, t-Butyl thioether, t-Butyl thiolester, TBDMS ester, TBDMSether, TBDPS ether, TES ether, THF ether, THP ether, TIPDS diether, TIPSether, TMS ester, TMS ether, TMS thioether, Tosyl hydrazone, TPS ether,Trifluoroacetamide.

A list of commercially available protecting groups may be found inSigma-Aldrich (2003) Catalog, the contents of which as it relates to thedisclosure of protective groups is incorporated by reference herein inits entirety.

In general, in one aspect of the invention, the protecting groups usedin the present invention may be those that are used in the sequentialaddition of one or more amino acids or suitably protected amino acids toa growing peptide chain. Normally, either the amino or carboxyl group ofthe first amino acid is protected by a suitable protecting group.

In a particularly preferred method the amino function is protected by anacid or base sensitive group. Such protecting groups should have theproperties of being stable to the conditions of linkage formation, whilebeing readily removable without destruction of the growingbranched/linear polymer. Such suitable protecting groups may be withoutlimitation 9-fluorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl(Boc), benzyloxycarbonyl (Cbz), biphenylisopropyl-oxycarbonyl,t-amyloxycarbonyl, isobornyloxycarbonyl, (α,α)-dimethyl-3,5-dimethoxybenzyloxycarbonyl, o-nitrophenylsulfenyl,2-cyano-t-butyloxycarbonyl, and the like.

Particularly preferred protecting groups also include2,2,5,7,8-pentamethylchroman-6-sulfonyl (pmc), p-toluenesulfonyl,4-methoxybenzenesulfonyl, adamantyloxycarbonyl, benzyl,o-bromobenzyloxycarbonyl, 2,6-dichlorobenzyl, isopropyl, t-butyl (t-Bu),cyclohexyl, cyclophenyl and acetyl (Ac), 1-butyl, benzyl andtetrahydropyranyl, benzyl, p-toluenesulfonyl and 2,4-dinitrophenyl.

In the addition method, the branched termini of the linear/branchedpolymer is attached to a suitable solid support. Suitable solid supportsuseful for the above synthesis are those materials which are inert tothe reagents and reaction conditions of the stepwisecondensation-deprotection reactions, as well as being insoluble in themedia used.

The removal of a protecting group such as Fmoc from the linear tip ofthe branched/linear polymer may be accomplished by treatment with asecondary amine, preferably piperidine. The protected portion may beintroduced in about 3-fold molar excess and the coupling may bepreferably carried out in DMF. The coupling agent may be withoutlimitationO-benzotriazol-1-yl-N,N,N′,N′-tetramethyluroniumhexafluorophosphate(HBTU, 1 equiv.) and 1-hydroxy-benzotriazole (HOBT, 1 equiv.).

The polymer may be deprotected, either in succession or in a singleoperation. Removal of the polypeptide and deprotection can beaccomplished in a single operation by treating the substrate-boundpolypeptide with a cleavage reagent, for example thianisole, water,ethanedithiol and trifluoroacetic acid.

Table 1 below lists various types of exemplified compounds. However, itis to be understood that variations in X, L, W, R and T are encompassedby the present invention. TABLE 1 Representative and ExemplifiedMacromolecule Compounds Compound No. X L W R T  3-1 A NH—(CH₂)₃C(O) NHCH₂O(CH₂)₂C(O) OH  3-2 A NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OMe  3-3 BocNH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH  3-4 Boc NH—(CH₂)₃C(O) NHCH₂O(CH₂)₂C(O) OMe  3-5 A NH—(CH₂CH₂O)₂CH₂C(O) NH CH₂O(CH₂)₂C(O) OH  3-6A NH—(CH₂CH₂O)₂CH₂C(O) NH CH₂O(CH₂)₂C(O) OMe  6-1 A NH—(CH₂)₃C(O) NHCH₂O(CH₂)₂C(O) OH  6-2 Boc NH-(cyclohexyl)(CO) CH₂(CH2)₂-(cyclohexyl)-C(O) NH₂  6-3 Boc NH—(CH₂CH₂O)₂CH₂C(O) NHCH₂O(CH₂)₂C(O) OH  6-4 Fmoc NH—(CH₂)₆NHC(O) NH CH₂—C═C—CH₂C(O) OH  6-5Fmoc NH—(CH₂)₇C(O) O CH₂—C═C—CH₂C(O) OMe  6-6 NS NH-(cyclohexyl)(CO) OCH₂O(CH₂)₂C(O) NH₂  6-7 NS NH—(CH₂)₆NHC(O) NH (CH2)₇ NH₂  8-1 ANH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH  8-2 Boc NH—(CH₂)₇C(O) NH (CH2)₂C(O)OH  8-3 NS NH—(CH₂)₆(CO) NH (CH2)₂-(cyclohexyl)-C(O) OH  8-4 FmocNH—(CH₂)₆(CO) O CH₂—C═C—CH₂C(O) NH₂  8-5 Fmoc NH—(CH₂)₆NH(CO) O(CH2)₂-(cyclohexyl)-C(O) OH  8-6 NS NH-(cyclohexyl)(CO) OCH₂OCH(CH₃)CH₂C(O) NH₂  8-7 Boc NH-(cyclopropyll)(CO) O CH₂—C═C—CH₂C(O)NH₂  9-1 A NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH  9-2 A NH—(CH₂)₃C(O) NHCH₂O(CH₂)₂C(O) OMe  9-3 A NH—(CH₂CH₂O)₂CH₂C(O) NH CH₂O(CH₂)₂C(O) OH  9-4A NH—(CH₂CH₂O)₂CH₂C(O) NH CH₂O(CH₂)₂C(O) OMe  9-5 Fmoc NH—(CH₂)₆C(O) NHCH₂O(CH₂)₂C(O) OH  9-6 Fmoc NH—(CH₂)₆C(O) NH CH₂O(CH₂)₂C(O) OMe  9-7 BocNH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH  9-8 Boc NH—(CH₂)₃C(O) NHCH₂O(CH₂)₂C(O) OMe  9-9 Ns NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH  9-10 NsNH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OMe  9-11 A NH—(CH₂)₆NHC(O)CH₂ CH₂(CH2)₇ OBzl 12-1 A NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH 12-2 FmocNH—(CH₂)₆NHC(O) NH (CH2)₂-(cyclohexyl)-C(O) NH₂ 12-3 BocNH-(cyclohexyl)(CO) O CH₂—C═C—CH₂C(O) OMe 12-4 Boc NH—(CH₂)₅ NHCH₂OCH(CH₃)CH₂C(O) NH₂ 12-5 NS NH-(cyclopropyl)(CO) CH₂ (CH2)₂ NH₂ 12-6NS NH—(CH₂)₆C(O) O CH₂OCH₂CH(CH₃)C(O) NH₂ 12-7 Fmoc NH—(CH₂)₆NHC(O) OCH₂OCH(CH₃)CH₂C(O) NH₂ 16-1 Boc NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) NH₂ 16-2Boc NH-(cyclohexyl)(CO) CH₂ (CH2)₂-(cyclohexyl)-C(O) OH 16-3 FmocNH—(CH₂CH₂O)₂CH₂C(O) O CH₂O(CH₂)₂C(O) OH 16-4 Fmoc NH—(CH₂)₆NHC(O) NH(CH₂)₂-(cyclohexyl)-C(O) NH₂ 16-5 NS NH-(cyclohexyl)(CO) NHCH₂—C═C—CH₂C(O) OH 16-6 NS NH-(cyclopropyl)(CO) CH₂ CH₂O(CH₂)₂C(O) OMe16-7 A NH-(cyclopropyl)(CO) CH₂ CH₂OCH(CH₃)CH₂C(O) OH 16-8 ANH-(cyclopropyl)(CO) CH₂ CH₂OCH₂CH(CH₃)C(O) NH₂ 16-9 A NH—(CH₂)₅ OCH₂OCH₂CH(CH₃)C(O) OH 18-1 A NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH 18-2Fmoc NH-(cyclohexyl)(CO) O CH₂OCH(CH₃)CH₂C(O) NH₂ 18-3 BocNH-(cyclopropyl)(CO) O CH₂OCH₂CH(CH₃)C(O) NH₂ 18-4 FmocNH—(CH₂)₆NHC(O)CH₂ NH (CH2)₂-(cyclohexyl)-C(O) OH 18-5 NSNH—(CH₂)₆NHC(O) CH₂ CH₂—C═C—CH₂C(O) OMe 18-6 Boc NH—(CH₂)₅ OCH₂OCH₂CH(CH₃)C(O) NH₂ 27-1 A NH—(CH₂)₃C(O) NH CH₂O(CH₂)₂C(O) OH 27-2 ANH—(CH₂)₆NHC(O)CH₂ CH₂ (CH2)₇ OH 27-3 Fmoc NH—(CH₂CH₂O)₂CH₂C(O) O(CH2)₂-(cyclohexyl)-C(O) NH₂ 27-4 NS NH-(cyclopropyl)(CO) NH(CH2)₂-(cyclohexyl)-C(O) NH₂ 27-5 Boc NH-(cyclohexyl)(CO) CH₂CH₂OCH(CH₃)CH₂C(O) OMe 27-6 Fmoc NH—(CH₂)₅ O CH₂OCH₂CH(CH₃)C(O) NH₂

Target-Specific Ligand or Probe

The target-specific ligand, also known as probe, which is to be attachedto the linear end of the branched/linear polymer may include a varietyof compounds, including chemicals, biochemicals, bioactive compounds andso on. In this regard, the ligand may be nucleic acid, oligonucleotide,RNA, DNA, PNA, or aptamer. The oligonucleotide may be a naturallyoccurring nucleic acid or an analog thereof. Thus, the ligand may be apolypeptide composed of naturally occurring amino acids or syntheticamino acids. The ligand may be a combination of nucleic acid, aminoacid, carbohydrate or any other chemical so long as it is capable ofbeing attached to the linear portion of the branched/linear polymer. Inparticular, the ligand may also be a chemical, such as based on atriazine backbone, which may be used as a component in a combinatorialchemistry library, in particular, a triazine tagged library.

Substrate

The substrate may be any solid surface to which the branched/linearpolymer may bind through either covalent or ionic bond. The substratemay be functionalized so that binding may occur between the branchedtermini of the branched/linear polymer. The surface of the substrate maybe a variety of surfaces according to the needs of the practitioner inthe art. If a microarry or biochip format is desired then typicallyoxidized silicon wafer, fused silica or glass may be the substrate.Preferably, the substrate may be a glass slide. Other substrates mayinclude membrane filters such as but not limited to nitrocellulose ornylon. The substrate may be hydrophilic or polar, and may possessnegative or positive charge before or after coating.

Microarray

In order to improve the performance of DNA microarrays, issues such asprobe design, reaction conditions during spotting, hybridization andwashing conditions, suppression of non-specific binding, distancebetween the biomolecules and the surface, and the space between theimmobilized biomolecules should be considered. Because most of thesefactors are associated with the nature of the microarray surface,surface optimization has become one of the major goals in microarrayresearch. Whitesell and Chang showed that an alpha-helix formation ofimmobilized oligopeptides was encouraged on a space-controlled goldsurface (Whitesell et al., Science 261, 73-76 (1993)). We now reportthat a surface modified with the cone-shaped dendron can provide DNAmicroarrays with single nucleotide polymorphism (or SNP) discriminationefficiency close to the solution value (1:0.01) while concurrentlyreducing DNA non-specific binding.

FIG. 2 is a scheme showing the synthesis of a dendron. Various startingmaterial, intermediate compounds, and dendron compounds, wherein “X” maybe any protecting group, including anthracenemethyl (A), Boc, Fmoc, Nsand so forth. FIG. 3(a) shows modification of glass surface with adendron (FIG. 3 b) and selective hybridization of a fluorophore-taggedtarget oligonucleotide with a matched oligonucleotide probe whilediscriminating effectively a single base mismatched pair out on thedendron-modified surface.

A second generation branch dendron having surface reactive functionalgroups at the branch termini may be used, which self assembles andprovides appropriate space between them. Previous studies showed thatmultiple ionic attractions between cations on a glass substrate andanionic carboxylates at the dendron's termini successfully generated awell-behaved monolayer, and guaranteed an inter-ligand space over 24 Å(Hong et al., Langmuir 19, 2357-2365 (2003)). To facilitate deprotectionand increase the deprotected apex amine's reactivity, we modified thestructure as in FIG. 3 b. We also observed that covalent bond formationbetween the dendron's carboxylic acid groups and the surface hydroxylgroups is as effective as the ionic attraction, while also providingenhanced thermal stability. Moreover, an oligoetheral interlayer waseffective for suppressing non-specific oligonucleotide binding.

The hydroxylated substrate was prepared by using a previously reportedmethod (Maskis et al., Nucleic Acids Res. 20, 1679-1684 (1992)).Substrates including oxidized silicon wafer, fused silica, and glassslide, were modified with (3-glycidoxypropyl)methyldiethoxysilane(GPDES) and ethylene glycol (EG). The dendron was introduced to theabove substrates through a coupling reaction between the dendron'scarboxylic acid group and the substrate's hydroxyl group using1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC) or1,3-dicyclohexylcarbodiimide (DCC) in the presence of4-dimethylaminopyridine (DMAP) (Boden et al., J. Org. Chem. 50,2394-2395 (1985); Dhaon et al., J. Org. Chem. 47, 1962-1965 (1982)). Theincrease in thickness after the dendron introduction was 11±2 Å, whichwas comparable to the previous value observed for the ionic bonding(Hong et al., Langmuir 19, 2357-2365 (2003)). After the immobilization,an absorption peak arising from the anthracene moiety of the dendron wasobserved at 257 nm. The molecular layer is stable enough to show nochange in terms of thickness and absorption characteristics uponstirring in dimethylformamide for 1 d (FIG. 4). The topographical imagesobtained by tapping mode atomic force microscope (AFM) also showed thatthe resulting layer was very smooth and homogeneous without anyaggregates or holes (FIG. 5).

To be ready for DNA microarrays, the immobilized dendron was activatedto generate a primary amine group through deprotection process. Afterthe deprotection in 1.0 M trifluoroacetic acid (TFA) (Komblum et al., J.Org. Chem. 42, 399-400 (1977), the absorption peak at 257 nm disappearedwithout any other detrimental change of the surface properties (FIG. 4a). This observation demonstrated that the protecting group was removedsuccessfully without chemically damaging the layer while thickness wasslightly decreased due to the elimination of the protecting group.

After modification with di(N-succinimidyl)carbonate (DSC) according to apreviously established method (Beier et al., Nucleic Acids Res. 27,1970-1977 (1999)), probe oligonucleotides were immobilized onto theactivated surface of glass slide by spotting 50 mM sodium bicarbonatebuffer (10% dimethylsulfoxide (DMSO), pH 8.5) solution of theappropriate amine-tethered oligonucleotide (20 μM) using a Microsys 5100Microarrayer (Cartesian Technologies, Inc.) in a class 10,000 cleanroom. Typically, for substrates with a reactive amine surface group, athiol-tethered oligonucleotide and a heterobifunctional linker such assuccinimidyl 4-maleimido butyrate (SMB) orsulphosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate(SSMCC) are employed (Oh et al., Langmuir 18, 1764-1769 (2002); Frutoset al., Langmuir 16, 2192-2197 (2000)). In contrast, because thedendron-modified surface guarantees a certain distance among the aminefunctional groups, use of homobifunctional linkers such as DSC is notproblematic. As a result, an amine-tethered oligonucleotide can beutilized for spotting. Apart from the cost effectiveness, use of easilyoxidized thiol-tethered oligonucleotide can be avoided, although it ispossible that such thiol-tethered oligonucleotides may be useful undercertain conditions.

The DNA microarrays were fabricated to evaluate the discriminationefficiency between a complementary pair (A:T) and three internalsingle-base mismatched pairs (T:T, G:T, C:T). After spotting the probeoligonucleotides side by side in a 4 by 4 format, the microarray wasincubated in a humidity chamber (80% humidity) for 12 h to give theamine-tethered DNA sufficient reaction time. Slides were then stirred ina buffer solution (2× SSPE buffer (pH 7.4) containing 7.0 mM sodiumdodecylsulfate) at 37° C. for 3 h and in boiling water for 5 min toremove the non-specifically bound oligonucleotides. Finally, theDNA-functionalized microarray was dried under a stream of nitrogen forthe next step. For a fair comparison, different kinds of probes werespotted in a single plate.

For hybridization, a 15-base oligonucleotide (Target 1) or 45-baseoligonucleotide (Target 2) was used (FIG. 3 c). Hybridization wasperformed in the above washing buffer solution containing a targetoligonucleotide (1.0 nM) tagged with a Cy3 fluorescent dye at 50° C. for1 h using a GeneTAC™ HybStation (Genomic Solution, Inc.). The microarraywas rinsed with buffer solution at 37° C. four times for 1 min in orderto remove excess target oligonucleotide and dried with nitrogen. Thefluoresecence signal on each spot was measured with a ScanArray Lite(GSI Lumonics) and analyzed by Imagene 4.0 (Biodiscovery).

In the case of the 15-base target oligonucleotide, the image shows thatthere is a dramatic difference in the intensity between the matched andthe internal mismatched pairs (FIG. 6 a). The normalized fluorescencesignal ratios (or intensity ratios for one base internal-mismatched pairversus the perfectly matched pair, i.e., MM/PM) were 0.005, 0.008, and0.006 (T:T, G:T, and C:T internal mismatches) (FIG. 6 a and Table 2).The observed selectivity is significantly improved over conventionalmethods, and a large increase of the selectivity (20˜82 times) isrecorded in comparison with DNA microarrays on the generic surface(Table 2). Previously, we also observed a selectivity factor of1:0.19-0.57 for microarrays fabricated on various amine surfacesincluding a mixed self-assembled monolayer (i.e., mixed SAM)(Oh et al.,Langmuir 18, 1764-1769 (2002)). In addition, other investigatorsimproved the performance of DNA microarrays by modifying their surfaceand inventing better detection process, but none has reached thissignificantly improved ratio as far as a fluorescence detection methodis concerned (Zhao et al., J. Am. Chem. Soc. 125, 12531-12540 (2003);Chakrabarti et al., J. Am. Chem. Soc. 125, 12531-12540 (2003); Benterset al., Nucleic Acids Res. 30, e10 (2002); Guschin et al., AnalyticalBiochemistry 250, 203-211 (1997); Taton et al., Science 289, 1757-1760(2000); Wang et al., Nucleic Acids Res. 30, e61 (2002)). For example,successful discrimination ratio of 1:0.07 was reported for a threecomponent hybridization/detection system (capture/target/probe)(Zhao etal., J. Am. Chem. Soc. 125, 12531-12540 (2003)). Even when peptidenucleic acids (PNAs) capable of increasing the selectivity were used,the selectivity on gold thin film and gold nanoparticle were 1:0.14 and1:0.07, respectively (Chakrabarti et al., J. Am. Chem. Soc. 125,12531-12540 (2003)). TABLE 2 Normalized fluorescence signal ratioMatched Mismatched Mismatched Mismatched (A:T) (T:T) (G:T) (C:T)Dendron-modified surface, 15- 1 0.005 0.008 0.006 mer (Target 1 &Probe 1) Dendron-modified surface, 45- 1 0.006 0.009 0.009 mer (Target 2& Probe 1) APDES-modified surface, C₆ 1 0.41 0.38 0.26 spacer (Target 1& Probe 1) APDES-modified surface, (T)₃₀ 1 0.17 0.18 0.12 spacer (Target1 & Probe 2)

To simulate a more realistic system, a 45-base target oligonucleotidewas employed. The MM/PM ratios for T:T, G:T, and C:T internal mismatcheswere 0.006, 0.009, and 0.009 (FIG. 6 b and Table 2). This result showsthat outstanding selectivity holds for the longer targetoligonucleotides. It is believed that the efficacy of this DNAmicroarray should be attributed to the peculiarity of thedendron-modified surface, mesospacing between immobilized DNA strands.

For comparison, a DNA microarray was fabricated on the substratemodified with (3-aminopropyl)diethoxymethylsilane (APDES)(Oh et al.,Langmuir 18, 1764-1769 (2002)), which is a typical substrate for DNA orprotein microarrays. Its selectivity was tested using the same procedureand oligonucleotides as those for the dendron-modified DNA microarray,except for the use of 1,4-phenylenediisothiocyanate (PDITC) linker.Amine-tethered oligonucleotides were employed as described by Guo (Guoet al., Nucleic Acids Res. 22, 2121-2125 (1994)). The observed MM/PMratios for T:T, G:T, and C:T cases were 0.41, 0.38, and 0.26 (FIG. 6 cand Table 2). Use of DSC linker on the APDES-modified substrate resultedin high coefficient variance (CV) value (>20%), which represents thedegree of variation among the spots, and non-uniform fluorescenceintensity within each spot. On the other hand, PDITC linker assuredbetter coefficient variance (CV) value (<15%) and homogeneousfluorescence intensity within a single spot like those of thedendron-modified substrate with DSC linker (FIG. 7).

For additional comparison, probe 2 oligonucleotides having an extra(T)₃₀ spacer at the 5′ end of oligomer were utilized for SNPdiscrimination test. For this case, the probe with the extra spacer wasimmobilized on an APDES-modified surface. The observed MM/PM ratios forT:T, G:T, and C:T cases were 0.17, 0.18, and 0.12 (FIG. 6 d and Table2). The selectivity was significantly enhanced in comparison with thecase of probe DNA with a C₆ spacer, but still was largely inferior tothe dendron-modified DNA microarray.

Hybridization on the surface poses various complications, hurdles tocontrol and predict the microarray's screening performance precisely.Non-specific binding, steric and electrostatic effects, andenvironmental changes during the washing process should be considered inaddition to the melting temperature (Tm) of the duplex and the Gibbsfree energy for the duplex formation. Difference between the Gibbs freeenergy of the internal-mismatched pairs (T:T, G:T, and C:T internalmismatches of the 15-mer) and that of the perfectly matched pair insolution is 2.67, 1.75, and 3.05 kcal/mol at 50° C. Gibbs free energywas calculated with H_(Y)T_(HER)™ Software(http://ozone2.chem.wayne.edu). Therefore, the theoretical fluorescenceratios (MM/PM) are 0.016, 0.065, and 0.009 respectively. Also, study insolution phase with a molecular beacon showed that SNP discriminationratio was as low as 1:0.01 (Taton et al., Science 289, 1757-1760(2000)). These data strongly demonstrate that our dendron-modified DNAmicroarray represents an ideal case that reaches or even surpasses thethermodynamic limit. In particular, for the G:T case, the discriminationefficiency in the microarray format is better than the value calculatedfor the solution phase. The answer to which factors are main reasons forthe selectivity increase is yet to be investigated, but washingstringency may play a role.

-   -   p53 SNP Detection

In biological systems, the p53 tumor-suppressor gene plays key roles incell regulation, gene transcription, genomic stability, DNA repair, andapoptosis (see Velculescu et al, 1996, Clin. Chem., 42: 858-868, Harriset al, 1996, 88: 1442-1455, Sidransky et al, Annu, Rev. Med., 1996, 47:285-301). It has been reported that loss of wild-type function of p53can lead to cancer and p53 mutations are the most frequent geneticchanges in human cancer such as colon, and lung cancer (Greenblatt,1994, 54: 4855-4878).

DNA microarrays on [9]-acid dendron modified substrates were applied tothe detection of single mutation of p53 tumor suppressor gene in cancercell line. Target DNA samples (˜200-400 bases) which contain 175 codonwere prepared by random priming the genomic DNA templates and allowed tohybridize with dendron-modified substrates on which 18 mer probeoligonucleotides had been immobilized in a 10 by 1 format. The MM/PMratio for A:C, T:C, and C:C internal mismatches were 0.028, 0.031, and0.007 (FIG. 8 a). This result shows that the outstanding selectivityholds for real target DNAs.

The DNA microarrays on [27]-acid dendron modified substrates wereprepared using the same method as in the case of [9]-acid dendron whichis described above and applied to the detection of single mutation of175 codon of p53 tumor suppressor gene. The MM/PM ratio for A:C, T:C,and C:C internal mismatches were 0.066, 0.01, and 0.005 (FIG. 8 b). Thisresult indicates that the DNA microarrays on [27]-acid dendron modifiedsubstrates also show outstanding selectivity for the detection of singlemutation of real target DNAs.

Detection of 7 hot spot mutations of p53 gene using singledendron-modified surface.

The dendron-modified substrates were applied to the detection of singlemutation of p53 tumor suppressor gene in cancer cell line. Target DNAsamples (200-400 mer) which span 7 hot spot codons (175, 215, 216, 239,248, 273, and 282) were amplified from the DNA extracted from cancercells by random priming and allowed to hybridize with capture probes(oligonucleotides of 15˜25 mer) corresponding to 7 hot spot codons thathad been immobilized (FIGS. 9 a and 9 b). Excellent SNP discriminationefficiency was obtained.

We fabricated successfully DNA microarray of the highest fidelity byproviding mesospacing among the probe DNA, and found that SNPdiscrimination efficiency could be enhanced to reach or even surpass thesolution value. The observed discrimination efficiency will make thismethodology widely acceptable for very reliable high throughput genediagnosis. It is expected that this strategy can be applied to variousbioassays utilizing immobilized biomolecules.

Controlled Pore Glass Bead

Natural polymers such as dextran and agarose are the most frequentlyused chromatography supports for affinity chromatography. Sepharose 6B,4B, and 2B are chromatographic materials composed of cross-linkedagarose, which exhibit extremely low nonspecific adsorption. In spite oftheir wide use, agarose gel, typically in a bead shape, suffers somedrawbacks. For instance, the flow (or elution) rates are moderate due totheir soft nature, they cannot be dried or frozen since they shrinkseverely and essentially irreversibly, and they do not tolerate someorganic solvents (Cuatrecasas, P. J. Biol. Chem. 1970, 245, 3059-3065;Kim et al., Biochemistry 2002, 41, 3414-3421). In comparison, controlledpore glass (CPG) exhibits many exceptional properties for thesupport: 1) it is mechanically stable, 2) it has a fixed threedimensional structure; it does not swell or shrink upon change ofenvironment, 3) it is chemically stable from pH 1 to pH 14, 4) it isinert to a broad range of nucleophilic and electrophilic reagents, 4) itis stable against heating, 5) it exhibits excellent flow (or elution)properties, 6) it shows less tendency to adhere to surface ofcontainers. In addition, after a modification step, removal of reagentsand byproducts through washing is rapid and efficient. All of thesecharacteristics support potential usefulness in many fields such aspermeation chromatography, solid phase synthesis, affinity purification,and so on.

Pore size: Effective porosity of CPG toward an adsorbed molecule isdetermined by the accessibility of the guest to the host surface. To afirst approximation, the accessibility of CPG to a guest depends ongeometric factors, which are related to the relative size of the poresof the host compared to the size of the guest. If a guest has amolecular size that is larger than the pore openings leading to theinternal surface, adsorption and interactions can only occur with theexternal surface, which is much smaller than the internal surface areaof the investigated porous materials (Poschalko et al., J. Am. Chem.Soc. 2003, 125, 13415-13426; Ottaviani et al., J. Phys Chem. B. 2003,107, 2046-2053). From these considerations, the extent and strength ofadsorption of a guest onto CPG is expected to depend on the followingparameters: pore size of CPG, the total surface area of the host, andthe chemical composition of accessible surface of the host. In ourinvestigation, three kinds of GST fused protein (GST (28 kDa),GST-PX^(P47) (41 kDa), and GST-Munc18 fragment (98 kDa)) were employed.Molecular dimension of GST-Munc 18 should be similar to that of a fusedGST of 100 kDa, GST-DREF (140×140×93 Å³) (Hirose et al., J. Biol. Chem.1996, 271, 3930-3937; Zhan et al., Gene 2001, 218, 1-9). To achieve thebalance between pore size and surface area, porosity of the support hasto be optimized for each specific protein. Because it is known that CPGwith a pore size of approximately 50 nm allows the inclusion ofcomplexes of the complete range of molecular subunits normally found inproteins our investigation had been carried out with 50 nm CPG.Simultaneously, use of CPG with a larger pore (300 nm) confirmed theeffectiveness of the former CPG as far as the above proteins areconcerned (Collins et al., Anal. Biochem. 1973, 54, 47-53; Haller, W. J.Chromatogr. 1973, 85, 129-131).

Modification of Glutathione CPG (Sample E1, E3, A, CS, and CL): A keyconcern of affinity matrices is degree of nonspecific binding (or NSB).It is a ubiquitous problem in affinity purification and solid-phasesynthesis. In general, key factors to suppress nonspecific binding areto avoid the hydrogen bond donor groups and increase the hydrophilicityof matrices (Sigal et al, J. Am. Chem. Soc. 1998, 120, 3464-3473;Chapman et al., Langmuir 2000, 16, 6927-6936; Chapman et al., J. Am.Chem. Soc. 2000, 122, 8303-8304; Holmlin et al., Langmuir 2001, 17,2841-2850; Ostuni et al., Langmuir 2001, 17, 6336-6343; Chapman et al.,Langmuir 2001, 17, 1225-1233; Ostuni et al., Langmuir 2001, 17,5605-5620). CPG surface, even when modified with an aminoalkyl group, ispolar and retains partial negative charge (Hudson, D. J. Comb. Chem.1999, 1, 403-457). Use of a diepoxide as a spacer had been reported tobe responsible for the hydrophilic character of the matrix and theminimal nonspecific binding (Suen et al., Ind. Eng. Chem. Res. 2000, 39,478-487; Sundberg et al., J. Chromatogr. B. 1974, 90, 87-98; Shimizu etal., Nature Biotechnology 2000, 18, 877-881). Therefore, 1,4-butanedioldiglycidyl ether (or BUDGE) was employed for the modification leading tosample E1 and E3. The key features of the incorporation of BUDGE includegeneration of very stable ethereal bond against hydrolysis, the enhancedflexibility through a long spacer arm, full distance from the surface,and suppression of nonspecific binding to a certain extent. The lastadvantage can be explained by resembled structural motif with that ofpolyethylene glycol. Diepoxides can be utilized to link a molecule and asurface having a nucleophile, such as amine and thiol. During the ringopening process, stable carbon-heteroatom bond is generated as well as aβ-hydroxy group. Use of the linker before and after dendron modificationguarantees flexibility of the tethered GSH. The summarized modificationsteps are outlined in FIG. 10. For incorporation of the dendrons on thematrices, common reagents called EDC and NHS were used. Aftermodification with the dendrons, acetic anhydride was introduced intosystem to cap the remained amine functionality. Finally, matrices weretreated by 20% piperidine for 30 min to deblock the Fmoc group of thedendrons for the further modification. After elongation with BUDGE onemore time, GSH was immobilized by utilizing reaction between the thioland the epoxide.

As a control, sample A was prepared. Sequential modification with BUDGE,1,3-diaminopropane, and BUDGE gave surface materials that is exactlysame as E1 and E3 except absence of the dendrons. As before, GSH wasimmobilized by ring opening reaction between the epoxide and the thiol.Other control beads (Sample CL and CS) were prepared by using aheterobiofunctional linker called GMBS to link GSH and AMCPG orLCAA-CPG. While, AMPCPG has a short arm consisting C3 hydrocarbon at thesurface, LCAA-CPG has a long arm of C15 aliphatic chain. After amideformation with GMBS was allowed, the beads were treated with GSH.Addition of thiol group into maleimido group generated a covalent bondbetween carbon and sulfur atoms. The two-step treatment produced GSHimmobilized controlled pore glass beads, i.e. CS and CL, with covalentbonds.

Ligand Density Measurement: Due to the difficulties in measuring theamount of immobilized glutathione directly, an indirect method that theligand density was determined by measuring amount of dibenzofulvenereleased during the deprotection step was employed.9-Fluorenylmethoxycarbonyl (Fmoc) protecting group at the apex of thedendrons is stable against acids but is readily cleaved by a variety ofbases. In this study 20% piperidine in DMF is employed to deprotect theFmoc functional group. Piperidine forms an adduct with thedibenzofulvene, and the adduct absorbs at 301 nm (Øye et al., J. Phys.Chem. B. 2003, 107, 3496-3499). On the other hand, when the absorbanceof the collected solution appeared at 301 nm during the deprotectionstep with 20% piperidine, it indicated that the deprotection proceededas intended.

Ligand density obtained with this method is 8.3 μmol/g for E1, 5.6μmol/g for E3. The density is reduced by a factor of 11.1 uponmodification with F-moc(3)acid and the value is further reduced by afactor of 1.5 upon use of a larger dendron. Thus, in a specificembodiment of the invention, smaller dendrons were more effective atobtaining higher density than using larger dendrons.

GST Binding Assay: Binding characteristics of sample A, E1, and E3 wereexamined using purified GST and cell lysate (lane 2, 3, and 4 in FIG.11). Lane 1 shows successful preparation of lysate. It is evident thatthe three matrices bind purified GST effectively. When cell lysate wasintroduced into the beads (lane 5, 6, and 7), a significant differencewas observed between A and E1 or E3. For sample A, in spite ofincorporation of BUDGE linkers, serious nonspecific binding wasobserved. Interestingly, when the dendrons were introduced on thematrix, nonspecific protein binding was effectively suppressed. It isnoteworthy that self-assembly of either the dendron of the firstgeneration or the one of the second generation effectively suppressesnonspecific binding of the solid support, while an extended spacerbetween the dendron and GSH retains the activity of the tetheredtripeptide.

In FIG. 12, in one aspect of the invention, etheral and amide groupsconstitute the main backbone of the structure, and immobilization of thedendrons generates again amide bonds. Also, high coverage of thedendrons is also an important factor for the success.

The ligand density for E1 is 1.48 times higher than that for E3. Inother words, 148% of the ligand concentration was recorded for E1 (Table3). In order to examine the binding efficiency of both beads, the weightof the samples was adjusted to have the same number of GSH in eachsample. Densitometer showed that the ligand utilization for both caseswas quite close (29%, 31%). The larger spacing of E3 does not enhancethe binding efficiency of GST, probably because the examined protein islarger than the spacing of both E1 and E3 anyway. TABLE 3 Ligandconcentration and ligand utilization of sample E1 and E3. Ratio of theligand Percentage of Ligand density concentration ligand Samples(umol/g) (%) utilization (%) E1 8.3 148 29 E3 5.6 100 31

Control experiment: We found that density of GSH was 14.5 μmol/g for CS,11.9 μmol/g for CL. To compare efficacy of the beads in terms ofspecific binding of GST, captured proteins with CS (5.7 mg) and CL (7.0mg) beads were analyzed along with samples from E1 (10.0 mg) and E3(14.8 mg) beads. The utilized quantity was adjusted to have the samenumber of the GSH roughly. It is evident in the chromatogram (FIG. 13)CS and CL beads display poor selectivity as well as low bindingcapacity. The result stresses again importance of the dendron toguarantee not only improved accessibility of GST towards immobilized GSHbut effective suppression of nonspecific binding.

Molecular Weight Dependence. Because the dendron modification generatesa surface of controlled spacing between the immobilized ligands, bindingcapacity towards proteins of various molecular weights is intriguing. Inparticular, it is known that use of the second generation dendronguarantees a spacing over 24 angstrom (Cardona et al., J. Am. Chem. Soc.1998, 120, 4023-4024). For this particular test, GST protein (28 kDa),GST-PX^(p47) (41 kDa), and GST-munc-18 fragment (98 kDa) from thewild-type lysate were prepared. As shown in FIG. 14, binding capacity ofthe beads (E1, E3, and Sepharose 4B) decreases sharply as molecularweight of proteins increases. It is interesting to note that the degreeof decrease holds same for the three different cases. When bindingcapacity of E1 is set at 100% for GST, GST-PX^(p47) has a relativebiding capacity of 92% and 22% for GST-munc18. For E3 bead, 85% forformer protein and 23% for the latter protein are recorded. This strongdependence on protein molecular weight was also observed withglutathione Sepharose-4B. For glutathione Sepharose-4B, the bindingefficiencies are 104% and 17% for GST-PX^(p47) and GST-munc18,respectively. The only notable difference is a rather constant capacityfor GST and GST-PX^(p47) for this commercially available matrix. Thedifference might reflect heterogeneous spacing in Sepharose 4B. In thismaterial, diverse spacings between GSH exist so that the matrix bindsthe fused GST as efficiently as the pristine GST. For the much biggerprotein, GST-munc18, the spacings should be too small. In this regard,constant decrease of binding capacity of the dendron-treated beadssupports again the regular spacing of GSH on the surface.

In summary, the dendron-modified matrix demonstrates selectivity as highas that of the commercial matrix (for example, Sepharose 4B), and almostsame molecular weight dependence as the commercial one. Theincorporation of the dendrons on AMPCPG matrix not only reduces thenonspecific binding effectively, but retains binding activity of GSH.Constant decrease of the binding capacity as increase of proteinmolecular weight was observed, and the phenomenon seems in harmony withthe regular spacing between the immobilized GSH. In addition to thewell-controlled spacing, favorable aspects such as mechanical stability,wide compatibility with various chemical environment, and easiness tohandle promise interesting applications.

The present invention is not to be limited in scope by the specificembodiments described herein. Indeed, various modifications of theinvention in addition to those described herein will become apparent tothose skilled in the art from the foregoing description and accompanyingfigures. Such modifications are intended to fall within the scope of theappended claims. The following examples are offered by way ofillustration of the present invention, and not by way of limitation.

EXAMPLES

Numbering scheme is used for compounds throughout the Examples such ascompound 1, compound 2, I, II, III, IV, V and so on. It is to beunderstood however, that the compound numbering scheme is consistentwith and is confined to the particular Example section to which it isrecited. For instance, compound 1 as recited in Example 2 may notnecessarily be the same compound 1 as found in Example 3.

Example 1 Methods For Making Microarray Using Size-ControlledMacromolecule

In Example 1, designations I, II, III, IV, and V refer to variouscompounds and intermediate compounds as shown in FIG. 2.

Example 1.1

Materials. The silane coupling reagents,(3-glycidoxypropyl)methyldiethoxysilane (GPDES) and(3-aminopropyl)diethoxymethylsilane (APDES), were purchased from Gelest,Inc. and all other chemicals were of reagent grade from Sigma-Aldrich.Reaction solvents for the silylation are anhydrous ones in Sure/Sealbottles from Aldrich. All washing solvents for the substrates are ofHPLC grade from Mallinckrodt Laboratory Chemicals. The UV grade fusedsilica plates (30 mm×10 mm×1.5 mm) were purchased from CVI LaserCorporation. The polished prime Si(100) wafers (dopant, phosphorus;resistivity, 1.5-2.1 Ω·cm) were purchased from MEMC ElectronicMaterials, Inc. Glass slides (2.5×7.5 cm) were purchased from CorningCo. All of the oligonucleotides were purchased from Metabion. Ultrapurewater (18 M Ω/cm) was obtained from a Milli-Q purification system(Millipore).

Example 1.2

Instruments. The film thickness was measured with a spectroscopicellipsometer (J. A. Woollam Co. Model M-44). UV-vis spectra wererecorded on a Hewlett-Packard diodearray 8453 spectrophotometer. Tappingmode AFM experiments were performed with a Nanoscope IIIa AFM (DigitalInstruments) equipped with an “E” type scanner.

Example 1.3

Cleaning the substrates. Substrates such as oxidized silicon wafer,fused silica, and glass slide, were immersed into Piranha solution(conc. H₂SO₄: 30% H₂O₂=7:3 (v/v)) and the reaction bottle containing thesolution and the substrates was sonicated for an hour. (Caution: Piranhasolution can oxidize organic materials explosively. Avoid contact withoxidizable materials.) The plates were washed and rinsed thoroughly witha copious amount of deionized water after the sonication. The cleansubstrates were dried in a vacuum chamber (30-40 mTorr) for the nextsteps.

Example 1.4

Preparing the hydroxylated substrates. The above clean substrates weresoaked in 160 ml toluene solution with 1.0 ml(3-glycidoxypropyl)methyldiethoxysilane (GPDES) for 10 h. After theself-assembly, the substrates were washed with toluene briefly, placedin an oven, and heated at 110° C. for 30 min. The plates were sonicatedin toluene, toluene-methanol (1:1 (v/v)), and methanol in a sequentialmanner for 3 min at each washing step. The washed plates were dried in avacuum chamber (30-40 mTorr). GPDES-modified substrates were soaked in aneat ethylene glycol (EG) solution with two or three drops of 95%sulfuric acid at 80-100° C. for 8 h. After cooling, the substrates weresonicated in ethanol and methanol in a sequential manner each for 3 min.The washed plates were dried in a vacuum chamber (30-40 mTorr).

Example 1.5

Preparing the dendron-modified substrates. The above hydroxylatedsubstrates were immersed into a methylene chloride solution dissolvingthe dendron (1.2 mM) and a coupling agent,1-[-3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC) or1,3-dicyclohexylcarbodiimide (DCC) (11 mM) in the presence of4-dimethylaminopyridine (DMAP) (0.82 mM). After 3 days at roomtemperature, the plates were sonicated in methanol, water, and methanolin a sequential manner each for 3 min. The washed plates were dried in avacuum chamber (30-40 mTorr) for the next step.

Example 1.6

Preparing the NHS-modified substrates. The dendron-modified substrateswere immersed into a methylene chloride solution with 1.0 Mtrifluoroacetic acid (TFA). After 3 h, they were again soaked in amethylene chloride solution with 20% (v/v) diisopropylethylamine (DIPEA)for 10 min. The plates were sonicated in methylene chloride and methanoleach for 3 min. After being dried in a vacuum chamber, the deprotectedsubstrates were incubated in the acetonitrile solution withdi(N-succinimidyl)carbonate (DSC) (25 mM) and DIPEA (1.0 mM). After 4 hreaction under nitrogen atmosphere, the plates were placed in a stirreddimethylformamide solution for 30 min and washed briefly with methanol.The washed plates were dried in a vacuum chamber (30-40 mTorr) for thenext step.

Example 1.7

Arraying oligonucleotides on the NHS-modified substrates. Probeoligonucleotides in 50 mM NaHCO3 buffer (pH 8.5) were spotted side byside in a 4 by 4 format on the NHS-modified substrate. The microarraywas incubated in a humidity chamber (80% humidity) for 12 h to give theamine-tethered DNA sufficient reaction time. Slides were then stirred ina hybridization buffer solution (2× SSPE buffer (pH 7.4) containing 7.0mM sodium dodecylsulfate) at 37° C. for 1 h and in boiling water for 5min to remove non-specifically bound oligonucleotides. Finally, theDNA-functionalized microarray was dried under a stream of nitrogen forthe next step. For a fair comparison, different kinds of probes werespotted in a single plate.

Example 1.8

Hybridization. Hybridization was performed in the hybridization buffersolution containing a target oligonucleotide (1.0 nM) tagged with a Cy3fluorescent dye at 50° C. for 1 h using a GeneTACTM HybStation (GenomicSolutions, Inc.). The microarray was rinsed with the hybridizationbuffer solution in order to remove excess target oligonucleotide anddried with nitrogen. The fluorescence signal on each spot was measuredwith a ScanArray Lite (GSI Lumonics) and analyzed by Imagene 4.0(Biodiscovery).

Example 1.9 Synthesis of the Dendron Example 1.9.1 Preparation of9-anthrylmethyl N-(3-carboxylpropyl)carbamate (1)—Compound I.

4-Aminobutyric acid (0.50 g, 4.8 mmol, 1.0 equiv) and triethylamine(TEA) (1.0 ml, 7.3 mmol, 1.5 equiv) were dissolved inN,N-dimethylformamide (DMF) and stirred at 50° C. 9-Anthrylmethylp-nitrophenyl carbonate (1.81 g, 4.8 mmol, 1.0 equiv) was slowly addedwhile stirring. After stirring at 50° C. for 2 h, the solution wasevaporated to dryness, and the solution was basified with 0.50 N sodiumhydroxide (NaOH) solution. The aqueous solution was washed with ethylacetate (EA), stirred in an ice bath and acidified with dilutehydrochloric acid (HCl). After the product was extracted with EA, theorganic solution was dried with anhydrous MgSO₄, filtered andevaporated. The total weight of the resulting yellow powder was 1.06 gand the yield was 65%.

¹H NMR(CDCl₃)

δ 11.00-9.00(br, CH₂COOH, 1H), 8.41 (s, C₁₄H₉CH₂, 1H), 8.31 (d,C₁₄H₉CH₂, 2H), 7.97 (d, C₁₄H₉CH₂, 2H), 7.51 (t, C₁₄H₉CH₂, 2H), 7.46(t,C₁₄H₉CH₂, 2H), 6.08(s, C₁₄H₉CH₂O, 2H), 5.01 (t, OCONHCH₂, 1H), 3.23(q,NHCH₂CH₂, 2H), 2.34(t, CH₂CH₂COOH, 2H), 1.77(m, CH₂CH₂CH₂, 2H).

¹³C NMR(CDCl₃)

δ 178.5(CH₂COOH), 157.9(OCONH), 132.1 (C₁₄H₉CH₂), 131.7(C₁₄H₉CH₂),129.7(C₁₄H₉CH₂), 129.7(C₁₄H₉CH₂), 127.3(C₁₄H₉CH₂), 126.8(C₁₄H₉CH₂),125.8(C₁₄H₉CH₂), 124.6(C₁₄H₉CH₂), 60.2(C₁₄H₉CH₂), 41.0(NHCH₂CH₂),31.7(CH₂CH₂COOH), 25.6(CH₂CH₂CH₂).

Example 1.9.2 Preparation of 9-anthrylmethylN-{[(tris{[2-(methoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}propylcarbonate(II)—Compound II.

9-Anthrylmethyl N-(3-carboxylpropyl)carbamate (0.65 g, 1.93 mmol, 1.5equiv), 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride(EDC) (0.37 g, 1.93 mmol, 1.5 equiv), and 1-hydroxybenzotriazole hydrate(HOBT) (0.261 g, 1.93 mmol, 1.5 equiv) were dissolved in acetonitrileand stirred at room temperature. Tris{[(methoxycarbonyl)ethoxy]methyl}aminomethane (0.49 g, 1.29 mmol, 1.0 equiv) dissolved in acetonitrilewas added with stirring, After stirring at room temperature for 12 h,the acetonitrile was evaporated. The crude product was dissolved in EAand washed with 1.0 N HCl and saturated sodium bicarbonate solution.After being dried with anhydrous MgSO₄, filtered, and evaporated, thecrude product was loaded in a column packed with silica gel.Purification by column chromatography (eluent: ethyl acetate:hexane=5:1(v/v)) resulted in a viscous yellow liquid. The total weight of theyellow liquid was 0.67 g, and the yield was 74%.

¹H NMR(CDCl₃)

δ 8.43(s, C₁₄H₉CH₂, 1H), 8.36(d, C₁₄H₉CH₂, 2H), 7.99 (d, C₁₄H₉CH₂, 2H),7.53(t, C₁₄H₉CH₂, 2H), 7.47(t, C₁₄H₉CH₂, 2H), 6.15(s, CONHC, 1H),6.08(s, C₁₄H₉CH₂O, 2H), 5.44(t, OCONHCH₂, 1H), 3.63-3.55(m,CH₂OCH₂CH₂COOCH₃, 21H), 3.27(q, NHCH₂CH₂, 2H), 2.46(t, CH₂CH₂COOCH₃,6H), 2.46(t, CH₂CH₂CONH, 2H), 1.81 (m, CH₂CH₂CH₂, 2H).

¹³C NMR(CDCl₃)

δ173.2(CH₂CONH), 172.7(CH₂COOCH₃), 157.4(OCONH), 132.9(C₁₄H₉CH₂),

131.5(C₁₄H₉CH₂), 129.5(C₁₄H₉CH₂), 129.4(C₁₄H₉CH_(2}, 127.5)(C₁₄H₉CH₂),127.0(C₁₄H₉CH₂), 125.6(C₁₄H₉CH₂), 124.7(C₁₄H₉CH₂), 69.6(NHCCH₂O),67.2(C₁₄H₉CH₂), 60.1 (OCH₂CH₂), 59.4(NHCCH₂), 52.1(OCH₃),40.8(NHCH₂CH₂), 35.1 (OCH₂CH₂), 34.7(CH₂CH₂CONH), 26.3(CH₂CH₂CH₂).

Anal. Calcd for C₃₆H₄₆N₂O₁₂ 0.5H₂O: C, 61.18; H, 6.65; N 4.03; Found:C61.09, H 6.69, N 3.96.

Example 1.9.3 Preparation of 9-anthrylmethylN-[({tris[(2-carboxyethoxy)methyl]methyl}amino)carbonyl]propylcarbamate(III)—Compound III.

9-AnthrylmethylN-{[(tris{[2-(methoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}propyl-carbonate(0.67 g, 0.93 mmol) was dissolved in acetone (30 ml) and 0.20 N NaOH (30ml, 6 mmol). After being stirred at room temperature for 1 d, theacetone was evaporated. The aqueous solution was washed with EA, stirredin an ice bath and acidified with dilute HCl. After the product wasextracted with EA, the organic solution was dried with anhydrous MgSO₄,filtered and evaporated. Solidification in acetone and ether solution at−20° C. resulted in a yellow powder. The total weight of the final paleyellow powder was 0.54 g with a yield of 88%.

¹H NMR(CDCl₃)

δ 11.00-9.00(br, CH₂COOH, 3H}, 8.61(s, C₁₄H₉CH₂, 1H}, 8.47(d, C₁₄H₉CH₂,2H), 8.11 (d, C₁₄H₉CH₂, 2H), 7.60(t, C₁₄H₉CH₂, 2H}, 7.52(t, C₁₄H₉CH₂,2H), 6.63(s, CONHC, 1H), 6.36(t, OCONHCH₂, 1H), 6.12(s, C₁₄H₉CH₂O, 2H).3.40-363(m, CH₂OCH₂CH₂COOH, 12H), 3.20(q, NHCH₂CH₂, 2H), 2.52(t,CH₂CH₂COOH, 6H), 2.17(t, CH₂CH₂CONH, 2H), 1.75(m, CH₂CH₂CH₂, 2H).

¹³C NMR(CDCl₃)

δ 172.2(CH₂COOH), 172.0(CH₂CONH), 156.7(OCONH), 131.2(C₁₄H₉CH₂),130.7(C₁₄H₉CH₂), 128.6(C₁₄H₉CH₂), 128.4(C₁₄H₉CH₂), 127.3(C₁₄H₉CH₂),126.2(C₁₄H₉CH₂), 124.8(C₁₄H₉CH₂), 124.0(C₁₄H₉CH₂), 68.6(NHCCH₂O),66.5(C₁₄H₉CH2), 59.5(0CH₂CH₂), 58.0(NHCCH₂), 40.0(NHCH₂CH₂),34.0(OCH₂CH₂), 33.5(CH₂CH₂CONH), 25.8(CH₂CH₂CH₂).

Anal. Calcd for C₃₃H₄₀N₂O₁₂ 1.5H₂O: C, 57.97; H 6.34; N 4.10; Found: C57.89; H 6.21; N 4.09.

Example 1.9.4 Preparation of 9-anthrylmethylN-[({tris[(2-{[(tris{[2-(methoxycarbonyl)ethoxy]methyl}(methyl)amino]carbonyl}ethoxy)methyl]methyl}amino)carbonyl]propylcarbamate(IV)—Compound IV.

9-Anthrylmethyl N-[({tris[(2-carboxyethoxy)methyl]methyl}amino)carbonyl]propylcarbamate (0.54 g, 0.82 mmol, 1.0 equiv), EDC (0.55g, 2.87 mmol, 3.5 equiv), and HOBT (0.39 g, 2.89 mmol, 3.5 equiv) weredissolved in acetonitrile and stirred at room temperature.Tris{[(methoxycarbonyl)ethoxy]methyl} aminomethane (0.96 g, 2.53 mmol,3.1 equiv) dissolved in acetonitrile was added with stirring. Afterstirring at room temperature for 36 h, the acetonitrile was evaporated.The crude product was dissolved in EA and washed with 1.0 N HCl andsaturated sodium bicarbonate solution. After drying with anhydrousMgSO₄, filtered, and evaporated, the crude product was loaded in acolumn packed with silica gel. Column purification (eluent: ethylacetate:methanol=20:1 (v/v)) resulted in a viscous yellow liquid. Thetotal weight of the yellow liquid was 1.26 g with an 88% yield.

¹H NMR(CDCl₃)

δ 8.47(s, C₁₄H₉CH₂, 1H), 8.39(d, C₁₄H₉CH₂, 2H), 8.02 (d, C₁₄H₉CH₂, 2H),7.53(t, C₁₄H₉CH₂, 2H), 7.47(t, C₁₄H₉CH₂, 2H), 6.60(s, CH₂CH₂CH₂CONHC,1H), 6.13(s, OCH₂CH₂CONHC, 3H), 6.11 (s, C₁₄H₉CH₂O, 2H), 5.79(t,OCONHCH₂ μl H), 3.65-3.60(m, CH₂OCH₂CH₂CONH, CH₂OCH₂CH₂COOCH₃, 75H),3.29(q, NHCH₂CH₂, 2H), 2.50(t, CH₂CH₂COOCH₃, 18H), 2.36(t, OCH₂CH₂CONH,6H), 2.27(t, CH₂CH₂CH₂CONH, 2H), 1.85(m, CH₂CH₂CH₂, 2H).

¹³C NMR(CDCl₃)

δ 173.3(OCH₂CH₂CONH), 172.5(CH₂CH₂CH₂CONH), 171.6(CH₂COOCH₃),157.2(OCONH), 131.8(C₁₄H₉CH₂), 131.5(C₁₄H₉CH₂), 129.4(C₁₄H₉CH₂),129.3(C₁₄H₉CH₂), 127.6(C₁₄H₉CH₂), 127.0(C₁₄H₉CH₂), 125.6(C₁₄H₉CH₂),124.7(C₁₄H₉CH₂), 69.5(NHCCH₂OCH₂CH₂COOCH₃), 67.9(NHCCH₂OCH₂CH₂CONH),67.2(C₁₄H₉CH₂), 60.3(OCH₂CH₂CONH), 60.2(OCH₂CH₂COOCH₃),59.2(NHCCH₂OCH₂CH₂COOCH₃, NHCCH₂OCH₂CH₂CONH), 52.1 (OCH₃),41.0(NHCH₂CH₂), 37.6(OCH₂CH₂CONH), 35.1 (OCH₂CH₂COOCH₃),34.7(CH₂CH₂CH₂CONH), 26.3(CH₂CH₂CH₂).

Anal. Calcd for C₈₁H₁₂₁N₅O₃₆.H₂O: C 55.31; H 7.05; N 3.98; Found: C55.05, H 7.08, N 4.04.

MALDI-TOF-MS: 1763.2 (MNa+), 1779.2 (MK+).

Example 1.9.5 Preparation of 9-anthrylmethylN-({[tris({2-[({tris[(2-carboxyethoxy)methyl]methyl}amino)carbonyl]ethoxy}methyl)methyl]amino}carbonyl)propylcarbamate(V)—Compound V.

9-AnthrylmethylN-[({tris[(2-{[(tris{[2-(methoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}ethoxy)methyl]methyl}amino)carbonyl]propylcarbamate (0.60 g, 0.34 mmol)was dissolved in acetone (30 ml) and 0.20 N NaOH (30 ml). After stirringat room temperature for 1 d, the acetone was evaporated. The aqueoussolution was washed with EA, stirred in an ice bath and acidified withdilute HCl. After the product was extracted with EA, the organicsolution was dried with anhydrous MgSO₄, filtered and evaporated. Thetotal weight of the final yellow powder was 0.37 g and the yield was68%.

¹H NMR(DMSO)

δ 13.00-11.00(br, CH₂COOH, 9H), 8.66(s, C₁₄H₉CH2, 1H), 8.42(d, C₁₄H₉CH₂,2H), 8.13 (d, C₁₄H₉CH2, 2H), 7.62(t, C₁₄H₉CH₂, 2H), 7.54(t, C₁₄H₉CH₂,2H), 7.12(t. OCONHCH₂, 1H), 7.10(s, OCH₂CH₂CONHC, 3H), 7.06(s,CH₂CH₂CH₂CONHC, 1H), 6.06(s, C₁₄H₉CH₂O, 2H), 3.57-3.55(m,CH₂OCH₂CH₂CONH, CH₂OCH₂CH₂COOH, 48H), 3.02(q, NHCH₂CH₂, 2H), 2.42(t,CH₂CH₂COOH, 18H), 2.32(t, OCH₂CH₂CONH, 6H), 2.11(t, CH₂CH₂CH₂CONH, 2H),1.60(m, CH₂CH₂CH₂, 2H).

¹³C NMR(DMSO)

δ 172.8(CH₂COOH), 172.2(CH₂CH₂CH₂CONH), 170.5(OCH₂CH₂CONH),156.5(OCONH), 131.0(C₁₄H₉CH₂), 130.6(C₁₄H₉CH₂), 129.0(C₁₄H₉CH₂),128.7(C₁₄H₉CH₂), 127.6(C₁₄H₉CH₂), 126.7(C₁₄H₉CH₂), 125.4(C₁₄H₉CH₂),124.3(C₁₄H₉CH₂), 68.3(NHCCH₂OCH₂CH₂COOH), 67.4(NHCCH₂OCH₂CH₂CONH),66.8(C₁₄H₉CH₂), 59.8(0CH₂CH₂COOH), 59.6(OCH₂CH₂CONH),57.9(NHCCH₂OCH₂CH₂CONH), 55.9(NHCCH₂OCH₂CH₂COOH), 36.4(NHCH₂CH₂),34.6(OCH₂CH₂COOH), 30.8(OCH₂CH₂CONH), 29.7(CH₂CH₂CH₂CONH),25.9(CH₂CH₂CH₂).

Example 2 Methods of Producing Alternative Starting Material DendronMacromolecule—Fmoc-Spacer-[9]-Acid

In Example 2, various indicated compounds are referred to as compound 1,2 and so forth.

First, we synthesized a spacer, 6-azidohexylamine (1) from1,6-dibromohexane according to Lee, J. W.; Jun, S. I.; Kim, K.Tetrahedron Lett., 2001, 42, 2709.

This spacer was attached to repeating unit (2) through unsymmetric ureaformation and made N₃-spacer-[3]ester (3). The repeating unit wassynthesized by condensation of TRIS with tert-butyl acrylate, which hadbeen reported in Cardona, C. M.; Gawley, R. E. J. Org. Chem. 2002, 67,141.

This triester was transformed to N₃-spacer-[3]acid (4) throughhydrolysis and coupled with triester (2) under peptide couplingconditions, which led to N₃-spacer-[9]ester. After reduction of azide toamine and protection of amine with Fmoc group, hydrolysis of nonaesterafforded Fmoc-spacer-[9]acid (5).

N-(6-Azidohexyl)-N′-tris{[2-(tert-butoxyearbonyl)ethoxy]methyl}-methylurea (3). Triphosgene (1.3g, 4.3 mmol) was dissolved in anhydrous CH₂Cl₂ (20 mL). A mixture of6-azidohexylamine (1) (1.6 g, 12 mmol) and N,N-diisopropylethylamine(DIEA, 2.4 mL, 13.8 mmol) in anhydrous CH₂Cl₂ (35 mL) was added dropwiseto the stirred solution of triphosgene over a period of 7 h using asyringe pump. After further stirring for 2 h, a solution of (2) (6.4 g,13 mmol) and DIEA (2.7 mL, 15.2 mmol) in anhydrous CH₂Cl₂ (20 mL) wasadded. The reaction mixture was stirred for 4 h at room temperatureunder nitrogen, and washed with 0.5 M HCl and brine. The organic layerwas then dried over anhydrous MgSO₄, and the solvent was removed byevacuation. Purification with column chromatography (silica, 1:1EtOAc/hexane) yielded colorless oil (3.0 g, 40%).

¹H NMR (CDCl₃, 300 MHz): δ 1.45 (s, (CH₃)₃C, 27H); 1.36-1.58 (m,CH₂CH₂CH₂CH₂, 8H); 2.46 (t, CH₂CH₂O, J=6.4 Hz, 6H), 3.13 (m, CONHCH₂,2H), 3.26 (t, N₃CH₂, J=6.9 Hz, 2H), 3.64-3.76 (m, CCH₂O and CH₂CH₂O,12H); 5.00 (t, CH₂NHCO, J=6.7 Hz, 1H), 5.29 (s, CONHC, 1H).

¹³C NMR (CDCl₃, 75 MHz): δ 26.52, 26.54, 28.81, 30.26 (CH₂CH₂CH₂CH₂);28.14((CH₃)₃C); 36.20 (CH₂CH₂O); 39.86 (CONHCH₂); 51.40 (N₃CH₂); 58.81(CCH₂O); 67.16 (CH₂CH₂O); 69.23 (CCH₂O); 80.58 ((CH₃)₃C); 157.96(NHCONH); 171.26 (COOt-Bu).

FAB-MS: 674.26 (M⁺).

N-(6-Azidohexyl)-N′-tris{[2-carboxyethoxy]methyl}methylurea (4).N₃-spacer-[3]ester (3) (0.36 g, 0.56 mmol) was stirred in 6.6 mL of 96%formic acid for 24 h. The formic acid was then removed at reducedpressure at 50° C. to produce colorless oil in a quantitative yield.

¹H NMR (CD₃COCD₃, 300 MHz): δ 1.34-1.60 (m, CH₂CH₂CH₂CH₂, 8H); 2.53 (t,CH₂CH₂O, J=6.4 Hz, 6H), 3.07 (t, CONHCH₂, J=6.9 Hz, 2H), 3.32 (t, N₃CH₂,J=6.9 Hz, 2H), 3.67-3.73 (m, CCH₂O and CH₂CH₂O, 12H).

¹³C NMR (CD₃COCD₃, 75 MHz): δ 27.21, 29.54, 31.02 (CH₂CH₂CH₂CH₂); 35.42(CH₂CH₂O); 40.27 (CONHCH₂); 52.00 (N₃CH₂); 59.74 (CCH₂O); 67.85(CH₂CH₂O); 70.96 (CCH₂O); 158.96 (NHCONH); 173.42 (COOH).

FAB-MS: 506.19 (MH⁺).

N-(6-Azidohexyl)-N′-tris[(2-{[(tris{[2-(tert-butoxycarbonyl)ethoxy]-methyl}methyl)amino]carbonyl}ethoxy)methyl]methylurea(4.1).

The HOBt (0.20 g, 1.5 mmol), DIEA (0.30 mL, 1.8 mmol), and EDC (0.33 g,1.8 mmol) were added to (4) (0.25 g, 0.50 mmol) in 5.0 mL of dryacetonitrile. Then, the amine (2) (1.14 g, 2.3 mmol) dissolved in 2.5 mLof dry acetonitrile was added, and the reaction mixture was stirredunder N₂ for 48 h. After removal of the solvent at reduced pressure, theresidue was dissolved in MC and washed with 0.5 M HCl and brine. Theorganic layer was then dried over MgSO₄, the solvent was removed invacuo, and column chromatography (SiO2, 2:1 EtOAc/hexane) yielded acolorless oil (0.67 g, 70%).

¹H NMR (CDCl₃, 300 MHz): δ 1.45 (s, (CH₃)₃C, 81H); 1.36-1.58 (m,CH₂CH₂CH₂CH₂, 8H); 2.40-2.47 (m, CH₂CH₂O gen. 1 & 2, 24H), 3.13 (m,CONHCH₂, 2H), 3.26 (t, N₃CH₂, 6.9 Hz, 2H), 3.62-3.69 (m, CCH₂O gen. 1 &2, CH₂CH₂O gen. 1 & 2, 48H); 5.36 (t, CH₂NHCO, J=6.7 Hz, 1H), 5.68 (br,CONHC, 1H), 6.28 (br, amide NH, 3H).

¹³C NMR (CDCl₃, 75 MHz): δ 26.59, 26.69, 28.91, 30.54 (CH₂CH₂CH₂CH₂);28.22 ((CH₃)₃C); 36.20 (CH₂CH₂O gen. 2); 37.43 (CH₂CH₂O gen. 1); 39.81(CONHCH₂); 51.47 (N₃CH₂); 58.93 (CCH₂O gen. 1); 59.89 (CCH₂O gen. 2);67.15 (CH₂CH₂O gen. 2); 67.68 (CH₂CH₂O gen. 1); 69.23 (CCH₂O gen. 2);70.12 (CCH₂O gen. 1); 80.57 ((CH₃)₃C); 158.25 (NHCONH); 171.01 (COOt-Bu)171.41 (CONH amides).

MALDI-MS: 1989.8 (MNa⁺), 2005.8 (MK⁺).

N-(6-Aminohexyl)-N′-tris[(2-{[(tris{[2-(tert-butoxycarbonyl)ethoxy]-methyl}methyl)amino]carbonyl}ethoxy)methyl]methylurea(4.2).

Nona-tert-butyl ester (4.1) (0.37 g, 0.20 mmol) was stirred with 10%Pd/C (37.0 mg) in ethanol (20.0 mL) under H₂ at room temperature for 12h. After checking completion of the reaction with TLC, the mixture wasfiltered with a 0.2 μm Millipore filter. After the filter paper wasrinsed with CH₂Cl₂, the combined solvent was removed in vacuo, andcolorless oil was recovered.

N-{6-(9-fluorenylmethoxycarbonyl)aminohexyl}-N′-tris[(2-{1[(tris{[2-(tert-butoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}ethoxy)methyl]methylurea(4.3).

The amine (4.2) (0.33 g, 0.17 mmol) and DIEA (33 μL, 0.19 mmol) weredissolved in 5.0 mL of CH₂Cl₂, and stirred for 30 min under nitrogenatmosphere. 9-Fluorenylmethyl chloroformate (48 mg, 0.19 mmol) in 2.0 mLof CH₂Cl₂ was added, and the reaction mixture was stirred for 3 h atroom temperature. The solvent was removed under reduced pressure andwashed with 0.5 M HCl and brine. The residue was purified with columnchromatography (silica, EtOAc) to yield colorless oil (0.18 g, 64%).

¹H NMR (CDCl₃, 300 MHz): δ 1.45(s, (CH₃)₃C, 81H); 1.23-1.58 (m,CH₂CH₂CH₂CH₂, 8H); 2.37-2.47 (m, CH₂CH₂O gen. 1 & 2, 24H); 3.10-3.22 (m,CONHCH₂, 4H); 3.62-3.70 (m, CCH₂O gen. 1 & 2, CH₂CH₂O gen. 1 & 2, 48H);4.22 (t, CH(fluorenyl)-CH₂, J=7.1 Hz, 1H); 4.36 (d, fluorenyl-CH₂, J=7.1Hz, 2H); 5.27-5.35 (m, CH₂NHCO, 2H); 5.67 (br, CONHC, 1H); 6.25 (br,amide, 3H); 7.28-7.77 (fluorenyl, 8H).

¹³C NMR (CDCl₃, 75 MHz): δ 26.85, 27.02, 30.27, 30.88 (CH₂CH₂CH₂CH₂);28.49 ((CH₃)₃C); 36.48 (CH₂CH₂O gen. 2); 37.73 (CH₂CH₂O gen. 1); 40.03,41.34 (CONHCH₂); 47.68 (CH(fluorenyl)-CH₂); 59.22 (CCH₂O gen. 1); 60.16(CCH₂O gen. 2); 66.87 (fluorenyl-CH₂); 67.43 (CH₂CH₂O gen. 2); 67.98(CH₂CH₂O gen. 1); 69.52 (CCH₂O gen. 2); 70.42 (CCH₂O gen. 1); 80.84((CH₃)₃C); 120.28, 125.52, 127.38, 127.98, 141.65, 144.48 (fluorenyl);156.88 (OCONH); 158.52 (NHCONH); 171.27 (COOt-Bu) 171.65(amide CONH).

MALDI-MS: 2186.8 (MNa⁺), 2002.8 (MK⁺).

N-{6-(9-fluorenylmethoxycarbonyl)aminohexyl}-N′-tris[(2-{[(tris{[2-carboxyethoxy]methyl}methyl)amino]carbonyl}ethoxy)methyl]-methylurea(5). Nona-tert-butyl ester having a protecting group (4.3) (0.12 g, 72mmol) was stirred in 10 mL of 96% formic acid for 18 h. The formic acidwas then removed at reduced pressure at 50° C. to produce colorless oilin a quantitative yield.

¹H NMR (CD₃COCD₃, 300 MHz): δ 1.23-1.51 (m, CH₂CH₂CH₂CH₂, 8H); 2.44-2.58(m, CH₂CH₂O gen. 1 & 2, 24H); 3.15-3.18 (m, CONHCH₂, 4H); 3.61-3.75 (m,CCH₂O gen. 1 & 2, CH₂CH₂O gen. 1 & 2, 48H); 4.23 (t, CH(fluorenyl)-CH₂,J=7.0 Hz, 1H); 4.35 (d, fluorenyl-CH₂, J=7.0 Hz, 2H); 5.85, 6.09 (br,CH₂NHCO, 2H); 6.57 (br, CONHC, 1H); 6.88 (br, amide NH, 3H); 7.31-7.88(fluorenyl, 8H).

¹³C NMR (CD₃COCD₃, 75 MHz): δ 27.21, 27.33, 30.69, 30.98 (CH₂CH₂CH₂CH₂);35.31 (CH₂CH₂O gen. 2); 37.83 (CH₂CH₂O gen. 1); 40.56, 41.54 (CONHCH₂);48.10 (CH(fluorenyl)-CH₂); 59.93 (CCH₂O gen. 1); 61.10 (CCH₂O gen. 2);66.86 (fluorenyl-CH₂); 67.81 (CH₂CH₂O gen. 2); 68.37 (CH₂CH₂O gen. 1);69.80 (CCH₂O gen. 2); 70.83 (CCH₂O gen. 1); 120.84, 126.13, 127.98,128.56, 142.10, 145.16 (fluorenyl); 157.50 (OCONH); 159.82 (NHCONH);173.20 (amide CONH); 173.93 (COOH).

EXAMPLE 3 Additional Dendron Compounds

It is to be noted that while a particular protecting group may be shownwith a macromolecule, the compounds are not limited to the specificprotecting groups shown. Moreover, while various chains and spacers aredepicted indicating an exact molecular structure, modifications arepossible according to accepted chemical modification methods to achievethe function of a density controlled, preferably low density, array on asubstrate surface. As a point of reference for the short-handdescription of the compounds, the left most letter(s) indicates theprotecting group; the numeral in brackets indicates the number ofbranched termini; and the right most chemical entity indicates thechemistry on the branched termini. For example, “A-[27]-acid” indicatesanthrylmethyl protecting group; 27 termini, and acid groups at thetermini.

A-[27]-acid

Boc-[1]-acid

Boc-[3]-ester

Boc-[3]-acid

Boc-[9]-ester

Boc-b [9]-acid

Ns-[9]-ester

Ns-[9]-acid

Fmoc-[9]-ester (R=t-butyl)

Fmoc-[9]-acid

AE-[1]-acid

AE-[3]-acid

AE-[9]-acid

A-[6]-acid

A-[8]-Acid

A-[12]-Acid

A-[16]-Acid

A-[18]-Acid

G. R. Newkome J. Org Chem. 1985, 50, 2003

J.-J. Lee Macromolecules 1994, 27, 4632

L. J. Twyman Tetrahedron Lett. 1994, 35, 4423

D. A. Tomalia Polym. J. 1985, 17, 117

E. Buhleier. Synthesis 1978, 155

A. W. van der Made J. Chem. Soc., Chem. Commun. 1992, 1400

G. R. Newkome Angew. Chem. Int. Ed. Engl. 1991, 30, 1176

G. R. Newkome Angew. Chem. Int. Ed. Engl. 1991, 30, 1176

K. L. Wooley J. Chem. Soc., Perkin Trans.l 1991, 1059

Example 3.1 Preparation Methods

1. A-[3]-OEt (3)

Compound 1 reacted with NaC(CO₂Et)₃ 2 in C₆H₆/DMF at 80° C.

2. A-[3]-OMe (5)

A-[3]-OEt 3 was reduced with LiAlH₄ or LiBH₄ in ether, reacted withchloroacetic acid in the presence of t-BuOK/t-BUOH, and esterified withMeOH.

3. A-[3]-OTs (7)

Reduction of A-[3]-OMe 5 with LiAlH₄ in ether yields triol compound 6,which is tosylated to compound 7.

4. A-[9]-OEt (8)

A-[3]-OTs 7 was treated with NaC(CO₂Et)₃ in C₆H₆-DMF to afford thedesired nonaester (compound 8)

5. A-[27]-OH (9)

A-[9]-OEt 8 was treated with tris(hydroxymethyl)aminomethane and K₂CO₃in DMSO at 70° C.

Example 3.2

1. Boc-[2]-OMe (3)

Compound 1 was reacted with methyl acrylate 2 in methanol solvent attemperature below 50° C. Excess reagents and solvent were removed underhigh vacuum at temperature below 55° C.

2. Boc-[4]-NH₂ (5)

Boc-[2]-OMe 3 was reacted with large excesses of ethylenediamine (EDA) 4in methanol solvent temperature below 50° C. Excess reagents and solventwere removed under high vacuum at temperature below 55° C.

3. Boc-[8]-OMe (6)

Boc-[4]-NH₂ 5 was reacted with methyl acrylate 2 in methanol solvent attemperature below 50° C. Excess reagents and solvent were removed underhigh vacuum at temperature below 55° C.

Example 3.3

1. Boc-[2]-OH (3)

Compound 1, 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimidehydrochloride (EDC), and 1-hydroxybenzotriazole hydrate (HOBT) weredissolved in acetonitrile and stirred at room temperature. L-glutamicacid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrilewas added with stirring, After stirring at room temperature for 12 h,the acetonitrile was evaporated. The crude product was dissolved in EAand washed with 1.0 N HCl and saturated sodium bicarbonate solution.After being dried with anhydrous MgSO₄, filtered, and evaporated, thecrude product was loaded in a column packed with silica gel.Purification by column chromatography (eluent: ethyl acetate:haxane)resulted in a viscous yellow liquid.

Compound 2 was hydrolyzed by NaOH solution. After being stirred at roomtemperature for 1 d, the organic liquid was evaporated. The aqueoussolution was washed with EA, stirred in an ice bath and acidified withdilute HCl. After the product was extracted with EA, the organicsolution was dried with anhydrous MgSO₄, filtered and evaporated.

2. Boc-[4]-OH (3)

Compound 3, 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimidehydrochloride (EDC), and 1-hydroxybenzotriazole hydrate (HOBT) weredissolved in acetonitrile and stirred at room temperature. L-glutamicacid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrilewas added with stirring, After stirring at room temperature for 12 h,the acetonitrile was evaporated. The crude product was dissolved in EAand washed with 1.0 N HCl and saturated sodium bicarbonate solution.After being dried with anhydrous MgSO₄, filtered, and evaporated, thecrude product was loaded in a column packed with silica gel.Purification by column chromatography (eluent: ethyl acetate:haxane)resulted in a viscous yellow liquid.

Compound 4 was hydrolyzed by NaOH solution. After being stirred at roomtemperature for 1 d, the organic liquid was evaporated. The aqueoussolution was washed with EA, stirred in an ice bath and acidified withdilute HCl. After the product was extracted with EA, the organicsolution was dried with anhydrous MgSO₄, filtered and evaporated.

3. Boc-[8]-OH (3)

Compound 5, 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimidehydrochloride (EDC), and 1-hydroxybenzotriazole hydrate (HOBT) weredissolved in acetonitrile and stirred at room temperature. L-glutamicacid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrilewas added with stirring, After stirring at room temperature for 12 h,the acetonitrile was evaporated. The crude product was dissolved in EAand washed with 1.0 N HCl and saturated sodium bicarbonate solution.After being dried with anhydrous MgSO₄, filtered, and evaporated, thecrude product was loaded in a column packed with silica gel.Purification by column chromatography (eluent: ethyl acetate:haxane)resulted in a viscous yellow liquid.

Compound 6 was hydrolyzed by NaOH solution. After being stirred at roomtemperature for 1 d, the organic liquid was evaporated. The aqueoussolution was washed with EA, stirred in an ice bath and acidified withdilute HCl. After the product was extracted with EA, the organicsolution was dried with anhydrous MgSO₄, filtered and evaporated.

Example 3.4

1. Boc-[2]-CN (3)

Compound 1 was dissolved at room temp. in acrylonitrile. Glacial aceticacid was added and the solution is heated under reflux for 24 h. Excessacrylonitrile was distilled off under vacuum, the residue was extractedwith chloroform, and added to concentrated ammonia solution. The organicphase was separated, washed with water, and dried with sodium sulfate.

2. Boc-[2]-NH₂ (4)

Boc-[2]-CN 3 was dissolved in methanol and cobalt (II) chloridehexahydrate was added. Sodium borohydride was added in portions. Theresultant mixture was stirred for 2 h at room temp. and then cautiouslyacidified with concentrated hydrochloric acid. The solvent was removedunder vacuum and concentrated. The organic phase was separated, washedwith water, and dried with sodium sulfate.

3. Boc-[4]-CN (5)

Boc-[2]-NH₂ 4 was dissolved at room temp. in acrylonitrile. Glacialacetic acid was added and the solution is heated under reflux for 24 h.Excess acrylonitrile was distilled off under vacuum, the residue wasextracted with chloroform, and added to concentrated ammonia solution.The organic phase was separated, washed with water, and dried withsodium sulfate.

4. Boc-[4]-NH₂ (6)

Boc-[4]-CN 5 was dissolved in methanol and cobalt (II) chloridehexahydrate was added. Sodium borohydride was added in portions. Theresultant mixture was stirred for 2 h at room temp. and then cautiouslyacidified with concentrated hydrochloric acid. The solvent was removedunder vacuum and concentrated. The organic phase was separated, washedwith water, and dried with sodium sulfate.

5. Boc-[8]-CN (7)

Boc-[4]-NH₂ 6 was dissolved at room temp. in acrylonitrile. Glacialacetic acid was added and the solution is heated under reflux for 24 h.Excess acrylonitrile was distilled off under vacuum, the residue wasextracted with chloroform, and added to concentrated ammonia solution.The organic phase was separated, washed with water, and dried withsodium sulfate.

6. Boc-[8]-NH₂ (8)

Boc-[8]-CN 7 was dissolved in methanol and cobalt (II) chloridehexahydrate was added. Sodium borohydride was added in portions. Theresultant mixture was stirred for 2 h at room temp. and then cautiouslyacidified with concentrated hydrochloric acid. The solvent was removedunder vacuum and concentrated. The organic phase was separated, washedwith water, and dried with sodium sulfate.

7. Boc-[16]-CN (9)

Boc-[8]-NH₂ 8 was dissolved at room temp. in acrylonitrile. Glacialacetic acid was added and the solution is heated under reflux for 24 h.Excess acrylonitrile was distilled off under vacuum, the residue wasextracted with chloroform, and added to concentrated ammonia solution.The organic phase was separated, washed with water, and dried withsodium sulfate.

7. Boc-[16]-NH₂ (10)

Boc-[16]-CN 9 was dissolved in methanol and cobalt (II) chloridehexahydrate was added. Sodium borohydride was added in portions. Theresultant mixture was stirred for 2 h at room temp. and then cautiouslyacidified with concentrated hydrochloric acid. The solvent was removedunder vacuum and concentrated. The organic phase was separated, washedwith water, and dried with sodium sulfate.

Example 3.5

1. A-[3]-Alkene (3)

A-[1]-SiCl₃ 1 was refluxed with 10% excess of allylmagnesium bromide indiethyl ether for 4 h, and cooled to 0° C. and hydrolyzed with 10%aqueous NH₄Cl. The organic layer was washed with water, dried MgSO₄ andconcentrated.

2. A-[3]-SiCl₃ (4)

A mixture of A-[3]-Alkene 3, HSiCl₃, and a common platinum-basedhydrosilylation catalyst, e.g. H2PtCl6 in propan-2-ol (Speier'scatalyst) or platinum divinylsiloxane complecx (Karstedt's catalyst),was stirred for 24 h at room temp. When the reaction was completed,excess HSiCl₃ was removed under vacuum.

3. A-[9]-Alkene (5)

A-[3]-SiCl₃ 4 was refluxed with 10% excess of allylmagnesium bromide indiethyl ether for 4 h, and cooled to 0° C. and hydrolyzed with 10%aqueous NH₄Cl. The organic layer was washed with water, dried MgSO₄ andconcentrated.

4. A-[9′-SiCl₃ (6)

A mixture of A-[9]-Alkene 5, HSiCl₃, and a common platinum-basedhydrosilylation catalyst, e.g. H2PtCl6 in propan-2-ol (Speier'scatalyst) or platinum divinylsiloxane complecx (Karstedt's catalyst),was stirred for 24 h at room temp. When the reaction was completed,excess HSiCl₃ was removed under vacuum.

EXAMPLE 3.6

1. [1]-acid-[3]-triol (3)

(a) The triol 1 was cyanoethylated affording the nitrile compound 2.Acrylonitrile, nBu₃SnH, and azobisisobutyronitrile was added in PhCH₃including compound 1 at 110° C. (b) The nitirle compound 2 washydrolyzed to give compound 3 with carboxylic acid cleanly in suchcondition as KOH, EtOH/H₂O, H₂O₂, Δ.

2. A-[3]-triol (5)

(c) [1]-acid-[3]-triol was linked with compound 4 through an amidecoupling reaction using 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimidehydrochloride (EDC) and 1-hydroxybenzotriazole hydrate (HOBT).

3. A-[3]-tribromide (6)

(d) The alcohol was used to synthesize tribromide by bromination withHBr/H₂SO₄ at 100° C.

4. [1]-CN-[3]-OBzl (8)

(e) The triol 1 was treated with benzyl chloride to give trisether usingMe₂SO and KOH. (f) The trisether 8 was cyanoethylated affording thenitrile compound 9. Acrylonitrile, nBu₃SnH, and azobisisobutyronitrilewas added in PhCH₃ including compound 8 at 110° C.

5. [1]-OH-[3]-OBzl (11)

(g) The nitirle compound 9 was hydrolyzed to give compound 10 withcarboxylic acid cleanly in such condition as KOH, EtOH/H₂O, H₂O₂, Δ. (h)The compound 10 with a carboxylic acid was proceeded with excess 1.0 MBH₃.THF solution to converse the acid into alcohol.

6. [1]-Alkyne-[3]-OBzl (13)

(i) The alcohol was transformed into chloride (CH₂Cl₂) with excess SOCl₂and a catalytic amount of pyridine. (j) The chloride was reacted withlithium acetylide ethylenediamine complex in dimethylsulphoxide at 40°C.

7. A-[3]-Alkyne-[9]-OBzl (14)

-   -   (k) The A-[3]-OBzl 6 was alkylated with 4 equivalents of        terminal alkyne building block 13, hexamethylphosphoric        rtriamide (HMPA), lithium diisopropylamide (LDA), and        tetramethylethylenediamine (TMED) at 0-40° C. for 1.5 h.

Example 3.7

1. A-[9]-OH (15)

A-[3]Alkyne-[9]-OBzl 14 was reduced and deprotected with Pd—C/H toproduce A-[9]OH 15 in EtOH and THF solution including 10% Pd—C/H at 60°C. for 4d.

2. A-[27]-COOH (17)

The alcohol was smoothly converted into the nonabromide employing SOBr₂in CH₂Cl₂ at 40° C. for 12 h. And then the nonabromide compound wasalkylated with 12 equivalents of [I]-Alkyne-[3]-OBzl 13 to give 49% ofA-[9]-Alkyne-[27]-OBzl 16. A-[9]-Alkyne-[27]-OBzl 16 were reduced anddeprotected in one step with Pd—C/H in EtOH and THF solution including10% Pd—C/H at 60□ for 4d yielding 89% of A-[27]-OH. A-[27]-OH wasoxidized by RuO₄ treating with NH₄OH or (CH₃)₄NOH to achieve 85% ofA-[27]-COOH 17.

Example 3.8

1) [G1]-(OMe)₂ (3)

A mixture of compound 1 (1.05 mol equiv.), 3,5-dimethoxybenzyl bromide(1.00 mol equiv. 2), potassium carbonate (1.1 mol equiv.) and 18-c-6(0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for48 h. The mixture was cooled and evaporated to dryness, and the residuewas partitioned between CH₂Cl₂ and water. The aqueous layer wasextracted with CH₂Cl₂ (3 x), and the combined organic layers were driedand evaporated to dryness. The crude product was purified by flashchromatography with EtOAc—CH₂Cl₂ as eluent to give compound 3.

2) [G1]-(OH)₂ (4)

Methyl ether group of compound 3 was deprotected by BBr₃ in EtOAcsolution for 1 h, and the crude product was purified by flashchromatography with MeOH-EtOAc as eluent to give compound 4.

3) [G2]-(OMe)₄ (5)

A mixture of [G1]-(OH)₂ (1.00 mol equiv. 4), 3,5-dimethoxybenzyl bromide(2.00 mol equiv. 2), potassium carbonate (2.1 mol equiv.) and 18-c-6(0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for48 h. The mixture was cooled and evaporated to dryness, and the residuewas partitioned between CH₂C1₂ and water. The aqueous layer wasextracted with CH₂Cl₂ (3 x), and the combined organic layers were driedand evaporated to dryness. The crude product was purified by flashchromatography with EtOAc—CH₂Cl₂ as eluent to give compound 5.

4) [G2]-(OH)₄ (6)

Methyl ether group of compound 5 was deprotected by BBr₃ in EtOAcsolution for 1 h, and the crude product was purified by flashchromatography with MeOH-EtOAc as eluent to give compound 4.

5) [G3]-(OMe)8 (7)

A mixture of [G2]-(OH)₄ (1.00 mol equiv. 6), 3,5-dimethoxybenzyl bromide(4.00 mol equiv. 2), potassium carbonate (4.1 mol equiv.) and 18-c-6(0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for48 h. The mixture was cooled and evaporated to dryness, and the residuewas partitioned between CH₂Cl₂ and water. The aqueous layer wasextracted with CH₂Cl₂ (3 x), and the combined organic layers were driedand evaporated to dryness. The crude product was purified by flashchromatography with EtOAc—CH₂Cl₂ as eluent to give compound 7.

6) G3]-(OH)₈ (8)

Methyl ether group of compound 7 was deprotected by BBr₃ in EtOAcsolution for 1 h, and the crude product was purified by flashchromatography with MeOH-EtOAc as eluent to give compound 8.

EXAMPLE 4 Assembly of the Dendron on a Substrate

TMAC (N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride) wasself-assembled on oxide glass instead of APDES. The dendrimer layer onTMAC layer did not need to cap the residual amine.

Aminosilylation with TMAC. Clean substrates (slide glass) were placedinto a solution of TMAC (2 mL) and acetone (100 mL) for 5 h. After theself-assembly, the substrates were taken out of the flask, washed withacetone. The substrates were placed in an oven, and heated at 110° C.for 40 min. After immersion in acetone, the substrates were sonicatedfor 3 min. The washed substrate was placed in a Teflon vessel, andplaced in a glass container with a big screw cap lined with an O-ring,and eventually the container was evacuated (30-40 mTorr) to dry thesubstrate.

Structure of TMAC (N-trimethoxysilylpropyl-N,N,N-trimethylammoniumchloride).

Self-assembly of the Fmoc-spacer-[9]acid was performed in same conditionto the case of CBz-[9]acid with exception of capping of the residualamines by acetic anhydride

Self-Assembly of the Fmoc-spacer-[9]acid (5). A certain amount of theFmoc-spacer-[9]acid (5) was dissolved in a mixed solvent (DMF:deionizedwater=1:1 (v/v)) to make a solution of 20 mL. The solution was addedinto a Teflon vessel, and subsequently pieces of the above preparedaminosilylated slide glass were placed in the solution. While allowingthe flask at room temperature to self-assemble, each piece of thesubstrate was taken out of the solution after 1 day. Right after beingtaken out, the plate was washed with a copious amount of deionizedwater. Each substrate was sonicated for 3 min in deionized water, amixture of deionized water-methanol (1:1 (v/v)), and methanol in asequential manner. After sonication, the substrates were placed in aTeflon vessel, and placed in a glass container with a big screw caplined with an O-ring, and eventually the container was evacuated (30-40mTorr) to dry the substrate.

Deprotection of Fmoc from the Self-Assembled Fmoc-spacer-[9]acid (5).Teflon vessels containing 5% piperidine in DMF were prepared. Theself-assembled substrates were immersed in the vessels, and stirred for20 min. Each substrate was sonicated for 3 min in acetone, and MeOH in asequential manner and evacuated in a vacuum chamber (30-40 mTorr).

Example 5 p53 Microarray on Dendron (9-acid and 27-acid) ModifiedSurface

Seven codons, 175, 215, 216, 239, 248, 273, and 282 which are alreadyknown to be missense mutational hotspots with unusually high frequencywere selected for this study. Codons 175, 248, 273, and 282 of 7 codonswere taken from the international TP53 mutation database (IARC,http//:www-p53.iarc.fr/p53DataBase.htm) and the other three codons 215,216, and 239 from Korean p53 mutational hotspot database. The captureprobe sequences (the DNA immobilized on dendron-modified surface) forseven codons were designed by software and their lengths were 15-23 mervaried from codon to codon to set Tm to around 55° C.

Example 5.1

Detection of 7 hot spot mutations of p53 gene using singledendron-modified surface The dendron-modified substrates were applied tothe detection of single mutation of p53 tumor suppressor gene in cancercell line. Target DNA samples (100-200 mer) which span 7 hot spot codons(175, 215, 216, 239, 248, 273, and 282) were amplified from the DNAextracted from cancer cells by random priming (See EXAMPLE 5.8) andallowed to hybridize with the capture probe (oligonucleotides of 15-25mer) corresponding to the 7 hot spot codons that had been immobilized.The fluorescence intensity of each hybridized spot was determined withconfocal laser scanner and the SNP discrimination efficiency wascalculated. This study shows the quality of DNA microarray ondendron-modified surface for the detection of single mutation in realtarget sample.

Example 5.2 Effect of Length of Probe Oligonucleotide with T30 onHybridization Efficiency and SNP Discrimination

The effect of the length of capture probe for the SNP discriminationefficiency was tested by varying the length of capture probes with T30.After immobilizing capture oligonucleotides corresponding to codons 175and 239 containing T30 by linking the 5′ end of the specific sequenceand the terminal primary amino group on dendron-modified surface, p53target DNA was hybridized and fluorescence intensity was measured. Thisstudy shows dependence of the SNP discrimination efficiency and signalintensity on the length of the capture probe.

Example 5.3 Concentration of Capture Probe vs. Intensity; andConcentration of Capture Probe vs. SNP Discrimination

Dependence of signal intensity and SNP discrimination efficiency on theconcentration of capture probes was investigated. Capture probes ondendron-modified surface, at various concentrations, were allowed tohybridize with target DNA and the fluorescence intensity and SNPdiscrimination efficiency were determined. Optimal concentration ofcapture probe for p53 was determined.

Example 5.4 Concentration of Target Probe vs. Intensity; andConcentration of Target Probe vs. SNP Discrimination

Dependence of signal intensity and SNP discrimination efficiency on theconcentration of target probes was investigated. Target DNAs of variousconcentration were applied to hybridization and the fluorescenceintensity and SNP discrimination efficiency were determined. This workprovides the dynamic range of DNA microarray on dendron-modifiedsurface.

Example 5.5 Detection of Mutation in Mixed Target Samples

Point mutations with target samples in which the mutated targetsequences exist in a small portion compared with normal sequence (5 or10%) may be detected. Samples containing two kinds of target DNAs wereprepared with different molar ratio and used for hybridization to detectsingle point mutation in certain codon in mixtures of normal as well asmutated target DNA. This work has clinical importance for detectingearly stage cancer.

Example 5.6 Detection of Mutation in Ten Unknown Colon Cancer Cell Lines

The inventive system is used to detect mutations in unknown cancer celllines.

Example 5.6.1

Cell cultures and genomic DNA extraction. The colon cancer cell linesSNU-C1, SNU-C5, COLO 201, COLO 205, DLD-1, LS 513, HCT-15, LS 174T, HCT116, and SW480 were purchased from KCLB (Korea Cell Line Bank, Seoul,Korea). Cells were cultured in RPMI 1640 supplemented with 10% fetalbovine serum (FBS), 100 μg/ml streptomycin and 100 U penicillin(GibcoBRL, Carlsbad, Calif.) and incubated in 5% CO₂ at 37° C. The coloncancer cells (2×10⁶ cells) were harvested for genomic DNA extraction byInvisorb® spin cell mini kit (Invitek, Berlin, Germany) following themanufacturer's instructions. From these genomic DNAs, p53 target DNAswere prepared (see EXAMPLE 5.8.2) and DNA microarray experiment wereperformed using the same procedure described above.

Example 5.7 Effect of Length of Target Probe on Hybridization Efficiencyand SNP Discrimination

By preparing different lengths of target DNAs by several differentmethods such as random priming, PCR, and DNase degradation the effect oflength of target probe on hybridization and SNP discriminationefficiency was investigated.

Example 5.8 Experimental Protocol Example 5.8.1 Genomic DNA Samples

Genomic DNAs of SNU-cell lines (SNU-61, 216, 475, 563, 601, 668, 761,and 1040) were kind gifts from Jae-Gab Park, College of Medicine inSeoul National University. The provided SNU-cell lines were humancarcinoma cell lines from individual Korean patients. Thecharacteristics of these cell lines were previously described and havebeen used in various studies (Bae I S et al., 2000, Park J G et al.,1997, Kang M S et al., 1996, Yuan Y et al., 1997, 378-87).

Example 5.8.2 Subcloning and Sequencing

-   -   p53 genes, especially between exon 5 and exon 8, for each cell        lines were amplified by PCR with 2 pairs of synthetic        oligonucleotide primers used in the previous report: Exon 5 Fwd        1,5′-CTG ACT TTC AAC TCT GTC TCC T-3′ (SEQ ID NO:5); Exon 5 Fwd        II, 5′-TAC TCC CCT GCC CTC AAC AA-3′ (SEQ ID NO:6); Exon 8 Rev        1,5′-TGC ACC CTT GGT CTC CTC CAC-3′ (SEQ ID NO:7); Exon 8 Rev        II, 5′-CTC GCT TAG TGC TCC CGG G-3′ (SEQ ID NO:8) (Kang M S et        al., 1996). Each genomic DNA was amplified with 10 pmoles of        first primer pair (exon 5 Fwd I and Exon 8 Rev I, corresponding        to intron 4 and intron 8), 250 μM dNTP mix, 2.5 U Taq polymerase        (NEB) in 1× ThermoPol buffer (supplemented with Taq polymerase)        for 20 μl of total reaction volume in Multiblock System (Hybaid,        UK) using the following settings: initiation activation of the        polymerase at 95° C. for 1 minute, then 20 cycles of 95° C. for        30 sec, 58° C. for 30 sec, 72° C. for 90 sec, followed by final        elongation step at 72° C. for 5 min. First PCR products were        diluted and used as template for second PCR. The amplified        genomic DNA PCR products were diluted 20 fold and used for the        second nested PCR under the same conditions as the previous step        except PCR was performed with 10 pmoles of the second primer        pair (exon 5 Fwd II and exon 8 Rev II, corresponding to exon 5        and exon 8) and the cycle for amplification was increased to 25        cycles. The final nested PCR products were purified by gel        extraction method. PCR products from genomic DNA were ligated        into pGEM T-easy vector (Promega) and transformed to DH5a cells.        Subcloned plasmid was purified by QIAGEN Plasmid Min kit (QIAGEN        Inc., Valencia, Calif.) for sequencing analysis. Bidirectional        sequencing was performed using pUC/M13 Forward and Reverse        Sequencing Primer as follows: M13 FWD 5′-GTT TTC CCA GTC ACG ACG        TTG-3′ (SEQ ID NO:9) and M13 REV 5′-TGA GCG GAT AAC AAT TTC ACA        CAG-3′ (SEQ ID NO:10).

Example 5.8.3 Preparation of Target Probe

DNA target probes spanning SNP sites were random primed and labeled in aMultiblock System (Hybaid, UK) using 50 ng of template DNA with 50 UKlenow enzyme (NEB), 1× EcoPol buffer supplemented with Klenow enzyme, 6μg of random octamer (synthesized by Bionics), low dT dNTP mix (100 μMdA,G,CTP/50 μM dTTP) and 50 μM Cyanine3-dUTP (NEN) in 20 μl of totalreaction volume at 37° C. for 2 hours. Unincorporated nucleotides wereseparated by QIAGEN MinElute PCR purification kit (QIAGEN Inc.,Valencia, Calif.). After quantitative and qualitative (specificactivity, number of nucleotide per an incorporated fluorescent dye)analysis using UV/Vis spectrophotometer, qualified products were appliedto the hybridization.

Example 5.8.4

Cell cultures and genomic DNA extraction. The colon cancer cell linesSNU-C1, SNU-C5, COLO 201, COLO 205, DLD-1, LS 513, HCT-15, LS 174T, HCT116, and SW480 were purchased from KCLB (Korea Cell Line Bank, Seoul,Korea). Cells were cultured in RPMI 1640 supplemented with 10% fetalbovine serum (FBS), 100 μg/ml streptomycin and 100 U penicillin(GibcoBRL, Carlsbad, Calif.) and incubated in 5% CO₂ at 37° C. The coloncancer cells (2×10⁶ cells) were harvested for genomic DNA extraction byInvisorb® spin cell mini kit (Invitek, Berlin, Germany) following themanufacturer's instructions.

Example 6 Fixing Protein Probe on the Dendron Example 6.1

Arraying NHS-biotin to the dendrimer modified slide glass. Produce thespotting solution of succinimidyl D-biotin (1.0 mg) in 1 mL sodiumbicarbonate buffer 50 mM and DMSO (40% v/v). Arraying NHS-biotin to thedendrimer modified slide glass was performed using Microsys 5100microarrayer (Cartesian Technologies, Inc, USA) in a class 10,000 cleanroom. After arraying and incubating for 1 h in a humidified chamber(˜75% humidity), the biotin microarrays were subsequently washed for 2 heach with DMF (50° C.) THF and aqueous wash with MBST (50 mM MES, 100 mMNaCl, 0.1% Tween-20, pH 6.0). Slides were rinsed with double-distilledwater, dried, and either used immediately or stored at room temperaturefor several days.

Example 6.2

Detection of protein/ligand interactions. This method according toHergenrother, P. J.; Depew, K. M.; Schreiber, S. L. J. Am. Chem. Soc.2000, 122, 7849 was followed. Before adding Cy3-labeled streptavidinsolution, the slides were blocked for 1 h with MBST supplemented with 3%bovine serum albumin (BSA). After a brief rinse, the slides were exposedto Cy3-labeled streptavidin solution for 30 min at room temperature.This solution was prepared by diluting stock solutions of theappropriate protein(s) with MBST supplemented with 1% BSA at aconcentration of 1 μg/mL. After incubation, the slides were rinsed oncewith MBST and then gently agitated with four changes of MBST over thecourse of 12 min. The slides was dried and scanned using a commercialconfocal laser scanner, ScanArray® Lite (GSI Lumonics). Quantitativemicroarray analysis software, ImaGene (BioDiscovery, Inc.) was used forimage acquisition and fluorescence intensity analysis.

EXAMPLE 7

Methods For Making Controlled Pore Glass Bead That IncludesSize-Controlled Macromolecule—Aminopropyl group tethered controlled poreglass beads (AMPCPG; 80-120 mesh; mean pore diameter, 50 nm or 300 nm)and controlled pore glass beads modified with a long chain aminoalkylgroup (LCAA-CPG; 80-120 mesh; mean pore diameter, 50 nm) were purchasedfrom CPG, Inc. 1,4-Butanediol diglycidyl ether, 1,3-diaminopropane,reduced glutathione (GSH), N-(3-methylaminopropyl)-N′-ethylcarbodiimide(EDC), N-hydroxysuccinimide (NHS),N-(9-fluorenylmethoxycarbonyloxy)chloride (Fmoc-Cl), piperidine,4-maleimidobutyric acid N-hydroxysuccinimide ester (GMBS), phosphatebuffered saline tablets (PBS) were obtained from Sigma-Aldrich. Allother chemicals were of analytical reagent grade and were used withoutfurther purification. Deionized water (18 MΩ·cm) was obtained by passingdistilled water through a Barnstead E-pure 3-Module system. UV-visspectra were recorded on a Hewlett-Packard diode-array 8453spectrophotometer.

Example 7.1

Immobilization of Glutathione on the Dendron-modified CPG (Sample E1 andE3). (i) Modification with Fmoc-(3)acid: AMPCPG (dry weight 0.70 g) waswashed thoroughly with acetone with a glass filter. After drying invacuum, a mixture of 1,4-butanediyl diglycidyl ether (1.0 mL) andcarbonate buffer solution (2.0 mL, pH=11) was added to AMPCPG (surfacecapacity: 91.8 μmol/g, surface area: 47.9 m²/g). After shaking for 24 hat room temperature, the resulting beads were separated from thesolution by filtration and washed thoroughly with deionized water andsubsequently with acetone. Then a vial containing this sample was shakenwith a mixture of 1,3-diaminopropane (1.0 mL) and carbonate buffersolution (pH=11) for 24 h at room temperature. After washing thoroughly,a mixture of 2-mercaptoethanol (1.0 mL) and aqueous sodium bicarbonatesolution (2.0 mL, pH=8.5) was employed for blocking the residual epoxygroup on the surface. Subsequently, an aqueous solution ofdimethylformamide (30% DMF (v/v)) dissolving Fmoc-(3)acid (14 mg, 21.3μmol), N-(3-methylaminopropyl)-N′-ethylcarbodiimide (15 mg, 77 μmol) andN-hydroxysuccinimide (9.0 mg, 77 μmol) was introduced into a vialcontaining the beads. After shaking for 11 h at room temperature, thebeads were washed thoroughly with deionized water and subsequently withacetone. (ii) Blocking step: Acetic anhydride (1.0 mL) in anhydrousmethylene chloride (2.0 mL) was allowed to react with the residual amineovernight at room temperature. (iii) Deprotection step: After washingthe beads with methylene chloride and subsequently with acetone, 20%piperidine in DMF (3.0 mL) was added in a vial holding the beads, andthe vial was shaken for 30 min. (iv) Ligand-immobilization step: Amixture of 1,4-butanediyl diglycidyl ether (1.0 mL) and carbonate buffersolution (2.0 mL, pH=11) was added again into the vial, and the mixturewas shaken for another 24 h at room temperature. After washing the beadswith deionized water and subsequently with acetone, the reducedglutathione (GSH, 5.4 mg, 17.6 μmol) in sodium bicarbonate solution (3.0mL, pH 8.5) was added into a vial containing the beads, and the vial wasshaken for 12 h at room temperature. After washing the beads, a mixtureof 2-mercaptoethanol (1.0 mL) and aqueous sodium bicarbonate solution(2.0 mL, pH=8.5) was added into the vial containing the beads. Finally,the beads were separated, washed, dried in vacuum, and stored at 4° C.under dry nitrogen atmosphere. The same steps were followed exactly toprepare the sample E3 as described above, except that Fmoc-(9) acid wasused instead of Fmoc-(3) acid.

Example 7.2

Preparation of Other GSH tethered Matrices for Control Experiment.(Sample CS, CL, and A): (i) Sample CS and CL: GSH was immobilizeddirectly on both AMPCPG and LCAA-CPG through GMBS linker. The beads(0.10 g) were washed thoroughly with acetone with a glass filter. Afterbeing dried in vacuum, a mixture of DMF and sodium bicarbonate buffer(1.0 mL, 3:7 (v/v), pH=8.5) dissolving 4-maleimidobutyric acidN-hydroxysuccinimide ester (GMBS, 3.0 mg, 11 μmol) was added into a vialcontaining the beads. After four hours of shaking at room temperature,the resulting beads were separated from the solution by filtration andwashed thoroughly with deionized water and subsequently with acetone.Finally, acetic anhydride (1.0 mL) in anhydrous methylene chloride (2.0mL) was allowed to react with residual amine group on the matrix. Afterthorough washing, glutathione (GSH, 3.4 mg, 11 μmol) in PBS buffer (1.0mL) was added into a vial containing the beads, and the vial was shakenfor 12 h at room temperature. After 2-mercaptoethanol (1.0 mL) was usedto block the residual maleimido group, the beads were separated, washed,dried in vacuum. (ii) Sample A: The same modification steps for E1 andE3 were followed to modify AMPCPG with 1,4-butanediyl diglycidyl etherand 1,3-diaminopropane. After the capping with 2-mercaptoethanol,1,4-butanediyl diglycidyl ether was employed to generate an epoxy group.Finally, glutathione was immobilized, and 2-mercaptoethanol was used toopen the remaining epoxy group on the beads.

Example 7.3

Determination of Amine Density on the Modified Beads: Either modifiedbeads on the way to E1 or E3 or beads for control experiments (10 mg)were taken into an e-tube. In parallel, 9-fluorenylmethyl chloroformate(Fmoc-Cl, 1.75 mg) and Na₂CO₃ (1.45 mg) were placed into a separateglass vial, and a mixed solvent (2:1(v/v) 1,4-dioxane and water, 2.5 mL)was added to dissolve the reagents. One fifth of the solution was takenand transferred into the e-tube containing the beads. The tube wasplaced into a vial, and the vial was shaken for 12 h at roomtemperature. The beads were separated with a glass filter, and theporous materials were washed with deionized water and subsequently withacetone. After being dried in vacuum, 20% piperidine in DMF (0.50 mL)was added into an e-tube containing the beads. The beads were allowed toreact with piperidine for 30 min. Then the resulting solution from thetube was transferred carefully into a new e-tube, and the beads werewashed with 20% piperidine in DMF (0.25 mL) twice. All of the solutionwas added into the previous e-tube. Then the solution was mixed with acertain volume of methanol to adjust the absorbance. The absorbance at301 nm was measured using a UV/N is spectrometer, and a relevant solventwas used for the background correction. To increase reliability, themeasurements were carried out with five different samples.

For calibration, we prepared a series of the solution ofN-Fmoc-ethanolamine (or 9-fluorenylmethyl N-(2-hydroxyethyl)carbamate)(30 μM-70 μM) in 20% piperidine in DMF. After allowing 30 min for thereaction, the solutions containing dibenzofulvene were utilized formeasuring absorbance, and calculating the absorption coefficient.

Example 7.4

Preparation of GST Fusion Protein Lysate: GST-fusion proteins wereprepared as described before, Kim, J. H.; Lee, S.; Kim, J. H.; Lee, T.G.; Hirata, M.; Suh, P.-G.; Ryu, S. H.; Biochemistry 2002, 41,3414-3421, which is incorporated by reference herein in its entirety.For large scale cultures, the single colony containing a recombinantpGEX plasmid was incubated into 200 ml of 2×YTA medium. After growing tolog phase, gene expression was induced with IPTG for another 6 h.Subsequently, cells were pelleted by centrifugation and washed with 1×PBS. Then E. coli was lysed in 10 mL hypotonic buffer (20 mM Tris, 150mM NaCl, 1.0 mM MgCl₂, 1.0 mM EGTA, pH 7.4) containing 0.50 mM PMSF bythe sonicator. The proteins were obtained by the removal of insolublematerial.

Example 7.5

Binding assays: (i) The effect of chain length: The prepared beads CL(5.72 mg), CS (6.97 mg), E1 (10.0 mg), and E3 (14.8 mg) were incubatedseparately with the mixed solution including GST lysates in 0.8 mL ofthe incubation buffer (20 mM Tris, 150 mM NaCl, 1.0 mM MgCl₂, 1.0 mMEGTA, 1% TX-100, 0.10 mM PMSF, pH 7.4, 0.50 mM PMSF) for 1 h at 4° C.,washed with the 10 bed volume of incubation buffer for three times andthen 100 μL of the SDS-sample buffer was added. After the tubes werecooked for 5 min at 95° C., 20 μL samples were utilized for SDS-PAGE andthe gel was stained by CBB G-250 staining solution. (ii) Selectivity ofthe dendron-treated matrices: 10 mg of samples A, E1, and E3, as well as100 μg of purified GST or GST-fused protein lysate were used in thisexperiment. The other steps were same as described above.

Example 7.6

Elution of GST Fusion Proteins from Glutathione Sepharose-4B, E1 and E3:Glutathione Sepharose-4B, E1, and E3 were processed as described in‘Binding assays (i)’. The amount of the protein bound to beads wasdetermined using Image gauge V3.12 (FUJI PHOTO FILM CO., LTD.). The samesteps were followed for PX domain of p47^(phox) and Munc-18 fragmentlysates (FIG. 13).

All of the references cited herein are incorporated by reference intheir entirety.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention specifically described herein. Suchequivalents are intended to be encompassed in the scope of the claims.

1. A substrate comprising a molecular layer of regularly spacedsize-controlled macromolecules comprising a polymer comprising branchedand linear regions in which a plurality of termini on the branchedregion are bound to the substrate, and a terminus of the linear regionis functionalized.
 2. The substrate according to claim 1, wherein themacromolecules are spaced at regular intervals.
 3. The substrateaccording to claim 2, wherein said macromolecules are spaced at regularintervals between about 0.1 nm and about 100 nm between the linearfunctionalized groups.
 4. The substrate according to claim 3, whereinsaid macromolecules are spaced at regular intervals of about 10 nm. 5.The substrate according to claim 1, wherein the terminus of the branchedregion is functionalized with —COZ, —NHR, —OR′, or —PR″₃, wherein Z is aleaving group, wherein R is an alkyl, wherein R′ is alkyl, aryl, orether, and R″ is H, alkyl, or alkoxy.
 6. The substrate according toclaim 5, wherein COZ is acid, ester, activated ester, acid halide,activated amide, or CO-imidazolyl.
 7. The substrate according to claim1, wherein the polymer is a dendron.
 8. The substrate according to claim1, wherein the linear region is comprised of a spacer region.
 9. Thesubstrate according to claim 8, wherein the spacer region is connectedto the branched region via a first functional group.
 10. The substrateaccording to claim 9, wherein the functional group is —NH₂, —OH, —PH₃,—COOH, —CHO, or —SH.
 11. The substrate according to claim 8, wherein thespacer region comprises a linker region covalently bound to the firstfunctional group.
 12. The substrate according to claim 11, wherein thelinker region comprises a substituted or unsubstituted alkyl, alkenyl,alkynyl, cycloalkyl, aryl, ether, polyether, ester, or aminoalkyl group.13. The substrate according to claim 8, wherein the spacer regioncomprises a second functional group.
 14. The substrate according toclaim 13, wherein the second functional group is —NH₂, —OH, —PH₃, —COOH,—CHO, or —SH.
 15. The substrate according to claim 13, wherein thesecond functional group is located at the terminus of the linear region.16. The substrate according to claim 1, wherein a protecting group isbound to the terminus of the linear region.
 17. The substrate accordingto claim 16, wherein the protecting group is acid labile or base labile.18. The substrate according to claim 1, wherein a target-specific ligandis bound to the terminus of the linear region.
 19. The substrateaccording to claim 18, wherein the target-specific ligand is a chemicalcompound, DNA, RNA, PNA, aptamer, peptide, polypeptide, carbohydrate,antibody, antigen, biomimetics, nucleotide analog, or a combinationthereof.
 20. The substrate according to claim 18, wherein the distancebetween target-specific ligands bound to the linear region of themacromolecules is from about 0.1 to about 100 nm.
 21. The substrateaccording to claim 1, wherein the substrate is made of semiconductor,synthetic organic metal, synthetic semiconductor, metal, alloy, plastic,silicon, silicate, glass, or ceramic.
 22. The substrate according toclaim 21, wherein the substrate is a slide, particle, bead, micro-well,or porous material.
 23. The substrate according to claim 22, wherein theporous material is a membrane, gelatin or hydrogel.
 24. The substrateaccording to claim 22, wherein the bead is a controlled pore bead.
 25. Amethod for manufacturing a molecular layer of regularly spacedsize-controlled macromolecules comprising a polymer comprising branchedand linear regions in which a plurality of termini on the branchedregion are bound to the substrate, and a terminus of the linear regionis functionalized, comprising (i) functionalizing the substrate so thatit will react with the termini of the macromolecules; and (ii)contacting the macromolecules to the substrate so that the termini andthe substrate form a bond.
 26. The method according to claim 25, whereinthe substrate is made of semiconductor, synthetic organic metal,synthetic semiconductor, metal, alloy, plastic, membrane, silicon,silicate, glass, or ceramic.
 27. The method according to claim 25,wherein said substrate is a slide, bead, microwell, or porous material.28. The method according to claim 27, wherein the porous material is ahydrogel, gelatin, or membrane.
 29. The method according to claim 27,wherein the bead is a controlled pore bead.
 30. The method according toclaim 25, wherein a target-specific ligand is fixed to the terminus ofthe linear region, comprising the steps of i) removing protecting groupfrom the terminus of the linear region of the macromolecules on thesubstrate; and ii) contacting the target-specific ligand or a linkermolecule linked to the target-specific ligand to the terminus of thelinear region of the macromolecules on the substrate so that the ligandor the linker molecule and the terminus form a bond, wherein the linkermolecule is a homobifunctional or heterobifunctional linker.
 31. Themethod according to claim 30, wherein the presence of saidmacromolecules on the substrate results in minimal interference in thebinding of said target-specific ligand to the linear termini.
 32. Themethod according to claim 30, wherein the presence of saidmacromolecules on the substrate results in minimal interference in thedetection of a target specific to said target-specific ligand.
 33. Themethod according to claim 30, wherein said target-specific ligand isspaced at regular intervals.
 34. The method according to claim 30,wherein said substrate comprises low density of the target-specificligands.
 35. The method according to claim 34, wherein the low densityof said target-specific ligands ranges from about 0.01 probe/nm² toabout 0.5 probe/nm²
 36. The method according to claim 30, wherein saidtarget-specific ligand is a chemical compound, DNA, RNA, PNA, aptamer,peptide, polypeptide, enzyme, carbohydrate, polysaccharide, antibody,antigen, biomimetics, nucleotide analog, or a combination thereof.
 37. Adiagnostic system for detecting a mutation in a gene, comprising thesubstrate according to claim 1, wherein the terminus of the linearregion is fixed with target specific oligonucleotides.
 38. Thediagnostic system according to claim 37, wherein the substrate comprisesoligonucleotides that are specific for cancer related genes.
 39. Thediagnostic system according to claim 38, wherein the cancer related geneis p53.
 40. A method for detecting presence of a mutation in a gene,comprising contacting the substrate according to claim 1 with a samplecontaining the gene to be assayed, wherein the terminus of the linearregion is fixed with a target specific oligonucleotide.
 41. The methodaccording to claim 40, wherein the gene is a cancer related gene. 42.The method according to claim 41, wherein the gene is p53.